http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=Hui+SunRiceWiki - User contributions [en]2026-05-27T08:02:07ZUser contributionsMediaWiki 1.30.0https://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180360OrfB2014-06-07T15:28:57Z<p>Hui Sun: /* Labs working on this gene */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref4" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
OrfB gene is located at the<br />
downstream of mitochondrial nad2 gene in the CMS.The<br />
novel orfB gene had high similarity with YMF19 family<br />
protein.In many cases, CMS-associated genes or<br />
sequences were caused by rearrangements of mitochondrial genomes resulting in the birth of new orfs composed of<br />
fragments of other mitochondrial respiratory-related genes<br />
or non-coding sequences <ref name="ref1" /><ref name="ref3" /><ref name="ref5" /> . Usually, such<br />
chimeric orfs were located at the flanking of mitochondrial<br />
respiratory/ATP synthesis-related genes and co-transcribed<br />
with these genes.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
<br />
==Labs working on this gene==<br />
*Advanced Laboratory for Plant Genetic Engineering (formerly IIT-BREF Biotek), Indian Institute of Technology, Kharagpur- 721302, India<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
<ref name="ref5"> Kempken F, Pring DR (1999) Male sterility in higher plantsfundamentals</ref><br />
and applications. Prog Bot 60:139–166<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180359OrfB2014-06-07T15:28:00Z<p>Hui Sun: /* Labs working on this gene */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref4" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
OrfB gene is located at the<br />
downstream of mitochondrial nad2 gene in the CMS.The<br />
novel orfB gene had high similarity with YMF19 family<br />
protein.In many cases, CMS-associated genes or<br />
sequences were caused by rearrangements of mitochondrial genomes resulting in the birth of new orfs composed of<br />
fragments of other mitochondrial respiratory-related genes<br />
or non-coding sequences <ref name="ref1" /><ref name="ref3" /><ref name="ref5" /> . Usually, such<br />
chimeric orfs were located at the flanking of mitochondrial<br />
respiratory/ATP synthesis-related genes and co-transcribed<br />
with these genes.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
<br />
==Labs working on this gene==<br />
*Advanced Laboratory for Plant Genetic Engineering (formerly IIT-BREF<br />
Biotek), Indian Institute of Technology, Kharagpur- 721302, India<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
<ref name="ref5"> Kempken F, Pring DR (1999) Male sterility in higher plantsfundamentals</ref><br />
and applications. Prog Bot 60:139–166<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180357OrfB2014-06-07T15:18:52Z<p>Hui Sun: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref4" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
OrfB gene is located at the<br />
downstream of mitochondrial nad2 gene in the CMS.The<br />
novel orfB gene had high similarity with YMF19 family<br />
protein.In many cases, CMS-associated genes or<br />
sequences were caused by rearrangements of mitochondrial genomes resulting in the birth of new orfs composed of<br />
fragments of other mitochondrial respiratory-related genes<br />
or non-coding sequences <ref name="ref1" /><ref name="ref3" /><ref name="ref5" /> . Usually, such<br />
chimeric orfs were located at the flanking of mitochondrial<br />
respiratory/ATP synthesis-related genes and co-transcribed<br />
with these genes.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
<ref name="ref5"> Kempken F, Pring DR (1999) Male sterility in higher plantsfundamentals</ref><br />
and applications. Prog Bot 60:139–166<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180356OrfB2014-06-07T15:17:49Z<p>Hui Sun: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref4" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
OrfB gene is located at the<br />
downstream of mitochondrial nad2 gene in the CMS.The<br />
novel orfB gene had high similarity with YMF19 family<br />
protein.In many cases, CMS-associated genes or<br />
sequences were caused by rearrangements of mitochondrial genomes resulting in the birth of new orfs composed of<br />
fragments of other mitochondrial respiratory-related genes<br />
or non-coding sequences <ref name="ref5" /><ref name="ref6" /><ref name="ref7" /> . Usually, such<br />
chimeric orfs were located at the flanking of mitochondrial<br />
respiratory/ATP synthesis-related genes and co-transcribed<br />
with these genes.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
<ref name="ref5"> Kempken F, Pring DR (1999) Male sterility in higher plantsfundamentals</ref><br />
and applications. Prog Bot 60:139–166<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180354OrfB2014-06-07T15:16:36Z<p>Hui Sun: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref4" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
OrfB gene is located at the<br />
downstream of mitochondrial nad2 gene in the CMS.The<br />
novel orfB gene had high similarity with YMF19 family<br />
protein.In many cases, CMS-associated genes or<br />
sequences were caused by rearrangements of mitochondrial genomes resulting in the birth of new orfs composed of<br />
fragments of other mitochondrial respiratory-related genes<br />
or non-coding sequences <ref name="ref5" /><ref name="ref6" /><ref name="ref7" /> . Usually, such<br />
chimeric orfs were located at the flanking of mitochondrial<br />
respiratory/ATP synthesis-related genes and co-transcribed<br />
with these genes.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180350OrfB2014-06-07T15:06:32Z<p>Hui Sun: /* Knowledge Extension */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref4" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180347OrfB2014-06-07T15:03:52Z<p>Hui Sun: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref4" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180343OrfB2014-06-07T15:00:26Z<p>Hui Sun: /* Mutation */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref4" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180340OrfB2014-06-07T14:59:58Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180338OrfB2014-06-07T14:59:07Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1,2,3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180337OrfB2014-06-07T14:58:44Z<p>Hui Sun: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1-3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<br />
<references><br />
<ref name="ref1"> Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic<br />
male sterility and fertility restoration. Trends Plant Sci 3:175–180</ref><br />
<ref name="ref2"> Budar F, Pelletier G (2001) Male sterility in plant: occurrence,<br />
determinism, significance and use. Life Sci 324:543–550</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S (2004) Interaction of mitochondrial and<br />
nuclear genes that affect male gametophyte development. PlantCell 16:S154–S169</ref><br />
<br />
<ref name="ref4">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180331OrfB2014-06-07T14:56:26Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1-3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180329OrfB2014-06-07T14:55:46Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1-3" />.<br />
[[File:suuu.jpg]]<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180328OrfB2014-06-07T14:54:59Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1-3" />.<br />
[[File:123.jpg]]<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180327OrfB2014-06-07T14:54:22Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
It is generally believed that the CMS trait is<br />
associated with mitochondrial DNA (mtDNA) rearrangements,<br />
which result from the expressions of chimeric open<br />
reading frames (orf) or alterations in genomic structure and<br />
transcriptions patterns of mitochondrial genes <ref name="ref1-3" />.<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180304OrfB2014-06-07T14:30:13Z<p>Hui Sun: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein.<br />
It is probobaly related with Cytoplasmic male sterility (CMS).<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C→T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180302OrfB2014-06-07T14:28:55Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein.<br />
It is probobaly related with Cytoplasmic male sterility (CMS).<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=180301OrfB2014-06-07T14:28:38Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
It is probobaly related with Cytoplasmic male sterility (CMS).<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179517OrfB2014-06-06T16:35:43Z<p>Hui Sun: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1">Srirupa Das, et al.An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS) system of<br />
Oryza sativa L. subsp. indica.BMC Plant Biology 2010, 10:39 </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179510OrfB2014-06-06T16:33:31Z<p>Hui Sun: /* Mutation */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<ref name="ref1" /><br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1"><br />
</ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179508OrfB2014-06-06T16:32:58Z<p>Hui Sun: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1"><br />
</ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179504OrfB2014-06-06T16:31:32Z<p>Hui Sun: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
<references><br />
<ref name="ref1"> Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell 2006, 18:515-517.</ref><br />
<ref name="ref2"> Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev Genet 1991, 25:461-486.</ref><br />
<ref name="ref3"> Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 2004, 16:154-169.</ref><br />
<ref name="ref4">Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci 1998, 3:175-180.</ref><br />
<ref name="ref5"> Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility restoration by nuclear genes. Molecular Biology and Biotechnology of <ref name="ref1">Plant Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622. </ref><br />
<ref name="ref6"> Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII mutant, a recombination-mediated change 5’ to the first exon of the mitochondrial nad1 gene is associated with lack of the NADH: ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem 1999, 216:361-370.</ref> <br />
<ref name="ref7"> Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genet 1997, 15:57-61.</ref><br />
<ref name="ref8"> </ref><br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179495OrfB2014-06-06T16:27:44Z<p>Hui Sun: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell 2006, 18:515-517.<br />
2. Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev Genet 1991, 25:461-486.<br />
3. Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 2004, 16:154-169.<br />
4. Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci 1998, 3:175-180.<br />
5. Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility restoration by nuclear genes. Molecular Biology and Biotechnology of Plant Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622. <br />
6. Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII mutant, a recombination-mediated change 5’ to the first exon of the mitochondrial nad1 gene is associated with lack of the NADH: ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem 1999, 216:361-370. <br />
7. Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genet 1997, 15:57-61.<br />
8.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179492OrfB2014-06-06T16:24:53Z<p>Hui Sun: /* Mutation */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<br />
RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites<br />
within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line.<br />
(b) The sterile line<br />
orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited<br />
as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell<br />
2006, 18:515-517.<br />
2. Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev<br />
Genet 1991, 25:461-486.<br />
3. Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes<br />
that affect male gametophyte development. Plant Cell 2004, 16:154-169.<br />
4. Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility<br />
and fertility restoration. Trends Plant Sci 1998, 3:175-180.<br />
5. Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility<br />
restoration by nuclear genes. Molecular Biology and Biotechnology of Plant<br />
Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622.<br />
6. Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII<br />
mutant, a recombination-mediated change 5’ to the first exon of the<br />
mitochondrial nad1 gene is associated with lack of the NADH:<br />
ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem<br />
1999, 216:361-370.<br />
7. Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial<br />
genome of Arabidopsis thaliana contains 57 genes in 366,924<br />
nucleotides. Nature Genet 1997, 15:57-61.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179481OrfB2014-06-06T16:11:42Z<p>Hui Sun: /* Mutation */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<br />
RFLPs were observed for the orfB gene (Figure 2A) in the mitochondrial genome between the sterile and the fertile lines. All restriction enzymes with the exception of EcoRI gave rise to a single hybridizing band with size variation between the sterile and fertile lines. Due to the presence of an EcoRI site in the orfB gene probe, digestion with EcoRI consistently generated two bands in all rice lines. The length of one band varied between the sterile and the fertile lines. Therefore, it was evident that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
[[Figure 1]]<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell<br />
2006, 18:515-517.<br />
2. Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev<br />
Genet 1991, 25:461-486.<br />
3. Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes<br />
that affect male gametophyte development. Plant Cell 2004, 16:154-169.<br />
4. Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility<br />
and fertility restoration. Trends Plant Sci 1998, 3:175-180.<br />
5. Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility<br />
restoration by nuclear genes. Molecular Biology and Biotechnology of Plant<br />
Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622.<br />
6. Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII<br />
mutant, a recombination-mediated change 5’ to the first exon of the<br />
mitochondrial nad1 gene is associated with lack of the NADH:<br />
ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem<br />
1999, 216:361-370.<br />
7. Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial<br />
genome of Arabidopsis thaliana contains 57 genes in 366,924<br />
nucleotides. Nature Genet 1997, 15:57-61.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179478OrfB2014-06-06T16:08:49Z<p>Hui Sun: /* Mutation */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<br />
RFLPs were observed for the orfB gene (Figure 2A) in the mitochondrial genome between the sterile and the fertile lines. All restriction enzymes with the exception of EcoRI gave rise to a single hybridizing band with size variation between the sterile and fertile lines. Due to the presence of an EcoRI site in the orfB gene probe, digestion with EcoRI consistently generated two bands in all rice lines. The length of one band varied between the sterile and the fertile lines. Therefore, it was evident that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell<br />
2006, 18:515-517.<br />
2. Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev<br />
Genet 1991, 25:461-486.<br />
3. Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes<br />
that affect male gametophyte development. Plant Cell 2004, 16:154-169.<br />
4. Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility<br />
and fertility restoration. Trends Plant Sci 1998, 3:175-180.<br />
5. Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility<br />
restoration by nuclear genes. Molecular Biology and Biotechnology of Plant<br />
Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622.<br />
6. Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII<br />
mutant, a recombination-mediated change 5’ to the first exon of the<br />
mitochondrial nad1 gene is associated with lack of the NADH:<br />
ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem<br />
1999, 216:361-370.<br />
7. Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial<br />
genome of Arabidopsis thaliana contains 57 genes in 366,924<br />
nucleotides. Nature Genet 1997, 15:57-61.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179471OrfB2014-06-06T16:02:58Z<p>Hui Sun: /* Mutation */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell<br />
2006, 18:515-517.<br />
2. Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev<br />
Genet 1991, 25:461-486.<br />
3. Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes<br />
that affect male gametophyte development. Plant Cell 2004, 16:154-169.<br />
4. Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility<br />
and fertility restoration. Trends Plant Sci 1998, 3:175-180.<br />
5. Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility<br />
restoration by nuclear genes. Molecular Biology and Biotechnology of Plant<br />
Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622.<br />
6. Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII<br />
mutant, a recombination-mediated change 5’ to the first exon of the<br />
mitochondrial nad1 gene is associated with lack of the NADH:<br />
ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem<br />
1999, 216:361-370.<br />
7. Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial<br />
genome of Arabidopsis thaliana contains 57 genes in 366,924<br />
nucleotides. Nature Genet 1997, 15:57-61.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179425OrfB2014-06-06T15:34:22Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Hypothetical protein<br />
<br />
===Mutation===<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell<br />
2006, 18:515-517.<br />
2. Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev<br />
Genet 1991, 25:461-486.<br />
3. Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes<br />
that affect male gametophyte development. Plant Cell 2004, 16:154-169.<br />
4. Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility<br />
and fertility restoration. Trends Plant Sci 1998, 3:175-180.<br />
5. Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility<br />
restoration by nuclear genes. Molecular Biology and Biotechnology of Plant<br />
Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622.<br />
6. Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII<br />
mutant, a recombination-mediated change 5’ to the first exon of the<br />
mitochondrial nad1 gene is associated with lack of the NADH:<br />
ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem<br />
1999, 216:361-370.<br />
7. Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial<br />
genome of Arabidopsis thaliana contains 57 genes in 366,924<br />
nucleotides. Nature Genet 1997, 15:57-61.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179400OrfB2014-06-06T15:19:23Z<p>Hui Sun: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
The editing of the orfB<br />
gene ~1.1 kb transcript co-segregated with fertility<br />
restoring alleles in a segregating population of F2 progeny<br />
of restored hybrid F1 plants.<br />
===Mutation===<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
=== Evolution ===<br />
=== Knowledge Extension ===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell<br />
2006, 18:515-517.<br />
2. Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev<br />
Genet 1991, 25:461-486.<br />
3. Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes<br />
that affect male gametophyte development. Plant Cell 2004, 16:154-169.<br />
4. Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility<br />
and fertility restoration. Trends Plant Sci 1998, 3:175-180.<br />
5. Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility<br />
restoration by nuclear genes. Molecular Biology and Biotechnology of Plant<br />
Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622.<br />
6. Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII<br />
mutant, a recombination-mediated change 5’ to the first exon of the<br />
mitochondrial nad1 gene is associated with lack of the NADH:<br />
ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem<br />
1999, 216:361-370.<br />
7. Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial<br />
genome of Arabidopsis thaliana contains 57 genes in 366,924<br />
nucleotides. Nature Genet 1997, 15:57-61.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179128OrfB2014-06-06T11:11:55Z<p>Hui Sun: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
The editing of the orfB<br />
gene ~1.1 kb transcript co-segregated with fertility<br />
restoring alleles in a segregating population of F2 progeny<br />
of restored hybrid F1 plants.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
1. Eckardt NA: Cytoplasmic male sterility and fertility restoration. Plant Cell<br />
2006, 18:515-517.<br />
2. Hanson MR: Plant mitochondrial mutation and male sterility. Annu Rev<br />
Genet 1991, 25:461-486.<br />
3. Hanson MR, Bentolila S: Interactions of mitochondrial and nuclear genes<br />
that affect male gametophyte development. Plant Cell 2004, 16:154-169.<br />
4. Schnable PS, Wise RP: The molecular basis of cytoplasmic male sterility<br />
and fertility restoration. Trends Plant Sci 1998, 3:175-180.<br />
5. Chase CD, Babay-Laughnan S: Cytoplasmic male sterility and fertility<br />
restoration by nuclear genes. Molecular Biology and Biotechnology of Plant<br />
Organelles Springer-VerlagDaniell H, Chase CD 2004, 593-622.<br />
6. Gutierres S, Combettes B, De Paepe R: In the Nicotiana sylvestris CMSII<br />
mutant, a recombination-mediated change 5’ to the first exon of the<br />
mitochondrial nad1 gene is associated with lack of the NADH:<br />
ubiquinone oxidoreductase (complex I) NADI subunit. Eur J Biochem<br />
1999, 216:361-370.<br />
7. Unseld M, Marienfeld JR, Brandt P, Brennicke A: The mitochondrial<br />
genome of Arabidopsis thaliana contains 57 genes in 366,924<br />
nucleotides. Nature Genet 1997, 15:57-61.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179125OrfB2014-06-06T11:11:11Z<p>Hui Sun: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
The editing of the orfB<br />
gene ~1.1 kb transcript co-segregated with fertility<br />
restoring alleles in a segregating population of F2 progeny<br />
of restored hybrid F1 plants.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
orfB transcripts of the sterile line have identical 3’ ends<br />
with that of transcripts from the fertile lines<br />
The basis of the observed differences in the orfB gene<br />
transcripts between the sterile and fertile lines was<br />
determined using 3’ RACE. The forward primer OGSP1<br />
(Figure 4) annealed 180 bp downstream of the<br />
initiation codon in the coding region of the orfB gene.<br />
In both the fertile and sterile rice lines, one amplified<br />
band of ~400 bp was obtained<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179124OrfB2014-06-06T11:09:54Z<p>Hui Sun: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
The editing of the orfB<br />
gene ~1.1 kb transcript co-segregated with fertility<br />
restoring alleles in a segregating population of F2 progeny<br />
of restored hybrid F1 plants.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
Editing of the orfB transcripts<br />
(a) The fertile line<br />
Mitochondrial RNA editing of the orfB transcript was<br />
assessed in the fertile rice line. Fourteen cDNA clones<br />
obtained from cDNA library of fertile rice line were<br />
sequenced. Determination of the orfB cDNA sequence<br />
from overlapping clones from the cDNA library showed<br />
four C®T conversions within the coding region relative<br />
to the orfB genomic sequence.<br />
<br />
===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179119OrfB2014-06-06T11:03:46Z<p>Hui Sun: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
The editing of the orfB<br />
gene ~1.1 kb transcript co-segregated with fertility<br />
restoring alleles in a segregating population of F2 progeny<br />
of restored hybrid F1 plants.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
<br />
===Evolution===<br />
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<br />
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==Labs working on this gene==<br />
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==References==<br />
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{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sunhttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=OrfB&diff=179090OrfB2014-06-06T10:22:02Z<p>Hui Sun: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Please input function information here.<br />
<br />
===Expression===<br />
Please input expression information here.<br />
<br />
===Evolution===<br />
Please input evolution information here.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
Please input cited references here.<br />
{{Mitochondrion|<br />
GeneName = orfB|<br />
Description = ORFB protein|<br />
Version = GeneID:6450152|<br />
Length = 468 bp|<br />
Definition = Oryza sativa Japonica Group ''orfB'', Mitochondrion gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Mitochondrion|Mitochondrion]]|<br />
AP = Mitochondrion:53424..53891|<br />
CDS = 53424..53891|<br />
GCID = <gbrowseImage3><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage3>|<br />
GSID = <gbrowseImage2><br />
name=NC_011033:53424..53891<br />
source=Rice_Japonica_Mitochondrion<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
AA = <aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>|<br />
DNA = <dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/gene?term=6450152 NCBI Gene:orfB]<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Mitochondrion]]<br />
[[Category:Mitochondrion]]</div>Hui Sun