Difference between revisions of "Os05g0595300"
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==Annotated Information== | ==Annotated Information== | ||
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| − | NRR gene is a single-copy gene located on chromosome 5, which contains four exons and three introns embedded in the protein-coding region<ref name="ref1"/>.NRR encodes two kinds of transcripts that have the same 5'end but differ in the location of their 3'ends: the longer transcripts terminate at the 3'UTR within the fourth exon, whereas the 3'ends of the shorter transcripts are situated in the second intron at a region of 165–204 bp from the donor splicing site. We have designated the longer and shorter transcripts as NRRa and NRRb, respectively. NRRa is composed of all the four exons and encodes a protein (NRRa) with 308-aa residues. NRRb contains only the first two exons and produces a 223-aa protein (NRRb), with the last residue valine derived from the first three nucleotides of intron 2. | + | NRR gene is a single-copy gene located on chromosome 5, which contains four exons and three introns embedded in the protein-coding region<ref name="ref1"/>.NRR encodes two kinds of transcripts that have the same 5'end but differ in the location of their 3'ends: the longer transcripts terminate at the 3'UTR within the fourth exon, whereas the 3'ends of the shorter transcripts are situated in the second intron at a region of 165–204 bp from the donor splicing site. We have designated the longer and shorter transcripts as NRRa and NRRb, respectively.[[File:Alternative splice.png|right|thumb|150px|"Schematic diagram of the generation of NRRa and NRRb from the primary NRR transcript.(from reference <ref name="ref1" />)."]] NRRa is composed of all the four exons and encodes a protein (NRRa) with 308-aa residues. NRRb contains only the first two exons and produces a 223-aa protein (NRRb), with the last residue valine derived from the first three nucleotides of intron 2. |
Revision as of 07:24, 27 May 2014
The rice NRR(nutrition response and root growth) gene responds to the deficiency of macronutrients and affects rice root growth.
Contents
Annotated Information
Function
NRR gene is a single-copy gene located on chromosome 5, which contains four exons and three introns embedded in the protein-coding region[1].NRR encodes two kinds of transcripts that have the same 5'end but differ in the location of their 3'ends: the longer transcripts terminate at the 3'UTR within the fourth exon, whereas the 3'ends of the shorter transcripts are situated in the second intron at a region of 165–204 bp from the donor splicing site. We have designated the longer and shorter transcripts as NRRa and NRRb, respectively.
Both NRRa and NRRb acting as the key components, modulate the rice root architecture with the availability of macronutrients.
GO assignment(s): GO:0048364
Expression
Expression of NRR in rice seedling roots was significantly influenced by deficiency of macronutrients. Knock-down of expression of NRRa or NRRb by RNA interference resulted in enhanced rice root growth. By contrast, overexpression of NRRa in rice exhibited significantly retarded root growth. These results revealed that both NRRa and NRRb played negative regulatory roles in rice root growth.
Evolution
No homologous protein was identified in rice following a BLAST search of the NCBI database with the deduced amino acid sequence of NRRa. However, NRRa-like proteins were found in Zea mays, Sorghum bicolor, Ricinus communis, Glycine max, Vitis vinifera, Medicago truncatula, Populus trichocarpa, Arabidopsis thaliana, and Physcomitrella. Those from monocotyledonous plants Zea mays and Sorghum bicolor shared sequence identities of 57.0–68.9% to NRRa, but those from dicotyledonous plants exhibited identities below 50%.
Amino acid sequence alignments of NRRa and NRRb with these homologous proteins showed that the conserved sequences were mainly located on five regions corresponding to the 55–80, 114–143, 178–189, 214–224, and 253–300-aa residues of NRRa, respectively.
Labs working on this gene
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- National Plant Gene Research Center, Beijing 100101, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
- Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing 100193, China
- Current address: School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- State Key Laboratory of Rice Biology, National Rice Research Institute, Hangzhou 310006 China
References
Structured Information
| Gene Name |
Os05g0595300 |
|---|---|
| Description |
Similar to CONSTANS-like protein |
| Version |
NM_001063049.1 GI:115465828 GeneID:4339814 |
| Length |
3633 bp |
| Definition |
Oryza sativa Japonica Group Os05g0595300, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 5:29738263..29741895 |
| Sequence Coding Region |
29738336..29738467,29739972..29740505,29740988..29741152,29741341..29741436 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008398:29738263..29741895 source=RiceChromosome05 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008398:29738263..29741895 source=RiceChromosome05 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgtacgccgccatgtacccggagaccttcggcttctctgcttacccccagcagcagcagccgccgcccgacgccgcctcctgcatctacaccaccgccttgccgctcatcgccgacccgcctgacatcctcggaaacatggcacaaccatcctttctatcagagtatgaccttggaggggaaggggacctgttcaaagctcctgaacccatcattgaagaaccagtgcttagccttgatccagttgcagcagccatttcgatgatgtctggcagtgagaacgtaatggatgaaactatagaggttgcagatatcagcgacattcagaatgactctcttttaagcgaagtattatacgagtgcgagaaggaactcatggagaagtccgcaatcgaagagactatttctgaactgctggacgtcaagattcctatgctgcaagtggaagagttccctagggaaacccaagtacaactaccggccatggagaaggagaagccatcagttcctgaatgttgttcactccagaaaagtgtcagttctgggtgcctcaactcagctgattggatcaatggaccagccaggccaaacttcctggacttccaaggattggactttgagacagcgtttgggttgaggagggcatacagcgaaggagacattcagaatcttggagctagcacccctcgacccgggaactcaggaaacgctcaattagcatcttgcgagaggcttgtaaccatcagtgacctgaaatctgaagaaaggaagcagaagctatctaggtacagaaagaagaaggtgaagagaaactttggcagaaagatcaagtatgcttgcaggaaggctcttgcagacagccagccaagagtgcgagggaggtttgccaagatcgaagaaggcgacttgctcaagccaaggaagtag</cdnaseq> |
| Protein Sequence |
<aaseq>MYAAMYPETFGFSAYPQQQQPPPDAASCIYTTALPLIADPPDIL GNMAQPSFLSEYDLGGEGDLFKAPEPIIEEPVLSLDPVAAAISMMSGSENVMDETIEV ADISDIQNDSLLSEVLYECEKELMEKSAIEETISELLDVKIPMLQVEEFPRETQVQLP AMEKEKPSVPECCSLQKSVSSGCLNSADWINGPARPNFLDFQGLDFETAFGLRRAYSE GDIQNLGASTPRPGNSGNAQLASCERLVTISDLKSEERKQKLSRYRKKKVKRNFGRKI KYACRKALADSQPRVRGRFAKIEEGDLLKPRK</aaseq> |
| Gene Sequence |
<dnaseqindica>74..205#1710..2243#2726..2890#3079..3174#gcttccgccttgttcaataatcaatatactcttctcctcgatctcttctcttgtccatctccaataattctccatgtacgccgccatgtacccggagaccttcggcttctctgcttacccccagcagcagcagccgccgcccgacgccgcctcctgcatctacaccaccgccttgccgctcatcgccgacccgcctgacatcctcgtgagctgcctcctcctcctccttccttgcacactagctaatccgcatgcatgtatccatggaatggattttcctctaatcgctctttctcttacccatggttcatgcatctgctctctctctctctctctttctctcatcacatcacacgtatgaagatatgaaatgaatgaagaaaaacagtcgctttctcttgttcctatttctttctgttttttcttgctccgttatgattaagatggcttgttggtccatgtactatctatgccaacaaaagccctcaataattcaccccttcactttcctcttttaagcaaagcaaccacaacatgtatgtacctcagacatttcatgagtgagatgactaatcgaatcgatccatccatcatccttaattgctgctgttgctttcctaatttctcttcaaacgcaaacgcttagctagcttcctaaacagagcaactaaaaattcactcactcacctttgagatttcttttcttcttccaccactactctactacatacatggcgtggcgaatgaatgaatgaattaattaaaattcatactctcacctttccttttcgcactcagctaataagcagctaagccaccgcgcgagtggtgcaagcaactggtcatgttggctgcaacttttcctttcctttttgtctttttcattcacatctttcttcctttttcatacttttttttctacttttctgcgcgcgcgcgcgcacacacatatattggtacatacatgcatcgcgcatgggttcagtctttgagatatttagtttagtggcagggaggggggatctaattaggttgagtcttaatagagcttttttggccaggatttctgatgcccctcctgtccatcagtatatgctctcggagcatgacagggacctgtaagttgacatgtactgcaccatcaacatactacatgcttgtagtcgtagatgtacccaaaaaaaaacaaaaaaacaagagagaggcatagcactacttgcaaatgcatccatatatactcacttttaattacttgccagccacactccacacacacactttgttattgcctcgcgcactgcttcctctcttctgcaatcttcccctcccctccccattgagagaggctacacttttctctactcaaattccctaggagtactttttttttctcgtcactctccttgccttaatttggagggaaaagaatatctacttactgctgtcgactcatgtagacaaaacaaaacaaagcacagtcattaatctgaccttaatatcttttggccttctctactttttttcccatagtaaaaataaattatgttttcactcctgaaacaaaaagtaaaatctactgaccagaaaatagaatgcttgttagtaacatgtttgcaattaagaacgttacatttcagtacttcattcattttaaaatgaattaactaagtggactgaaataacctctttgtcatctgtcgatcctacagggaaacatggcacaaccatcctttctatcagagtatgaccttggaggggaaggggacctgttcaaagctcctgaacccatcattgaagaaccagtgcttagccttgatccagttgcagcagccatttcgatgatgtctggcagtgagaacgtaatggatgaaactatagaggttgcagatatcagcgacattcagaatgactctcttttaagcgaagtattatacgagtgcgagaaggaactcatggagaagtccgcaatcgaagagactatttctgaactgctggacgtcaagattcctatgctgcaagtggaagagttccctagggaaacccaagtacaactaccggccatggagaaggagaagccatcagttcctgaatgttgttcactccagaaaagtgtcagttctgggtgcctcaactcagctgattggatcaatggaccagccaggccaaacttcctggacttccaaggattggactttgagacagcgtttgggttgaggagggcatacagcgaaggagacattcaggtttgatcatttttctcttgcggttatgttatgtacttactactgtatataggtaaggtagtgatagataaggaatcgttgtgagcaagcaacggctgtgtattgtaaagtgtgtttccgaaacacaggtgtcgagaaaagaaatcacctttgcccttgtatgtatatgtgcgtggtgcttctttactcaaattaaaggccatcaaagctatgacactgattttactatttctgcccaaagtaggccttttccttgtggttttaattttctttcaagatacttttacatgcaagctcctgcatacaaagttggtttctaagagactacctaggtgccaaagcgtacgtgtatatcctatggttttttgtttttatatactgtattattttagaaaggccgtgagattgttcgagtaaacatttgcagaccctgctaggttgttgaagaattgtacttacgatgctagttgtctttccaacagaatcttggagctagcacccctcgacccgggaactcaggaaacgctcaattagcatcttgcgagaggcttgtaaccatcagtgacctgaaatctgaagaaaggaagcagaagctatctaggtacagaaagaagaaggtgaagagaaactttggcagaaagatcaaggtaaaactatatattgtcctcttcctttttaatttttcaaagaaaagaaaaaagagaacataaggacagagaaggtactactacatgattaattagagaagctgattgaggctgatgaataatagtacaaacaaggagactgactgactgactgacactgactgatgcatcgtttggcatggttgcagtatgcttgcaggaaggctcttgcagacagccagccaagagtgcgagggaggtttgccaagatcgaagaaggcgacttgctcaagccaaggaagtagtaagaggaagaaacaaattaaagtaactcctggagaggacgagctgccagtgaaggaaggaaccttggcttctagaagcttctagctggtggaggaggaggaggaggaggaggaggagaggaaaggatccaaggtgcaaggcccagcctttgtgtgtagggggagggcgaggccaaggtggaagagaggcgccgtagtcgcggctgcacttgtcggaattaattttagctgctttggatcgtctccttctactactagactagtacttgtaattctattttccttccaatgcatgtgtaataataattagtaataatgctagtagtcggtattacttgctgcgagctgaaggccgcccatccatgtacaaatggctcgatgaagaaacttatcactagtagtaataaacttcagctcccttcaggcttcgcactggcactggaaggcatccattatctc</dnaseqindica> |
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