Difference between revisions of "NONHSAT122914"
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==Annotated Information==
===Transcriptomic Nomeclature===
Please input transcriptomic nomeclature information here.
===Functio...") |
Chunlei Yu (talk | contribs) (→References) |
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==Annotated Information== | ==Annotated Information== | ||
| − | === | + | ===Name=== |
| − | + | ST7OT | |
| + | |||
| + | ===Characteristics=== | ||
| + | Four noncoding RNAs from the RAY1/ST7 gene locus. Complex gene locus with a large number of coding and noncoding isoforms. ST7OT1 & 2 are antisense to ST7. ST7OT3 & 4 are on the sense strand. ST7OT1 - ~2kb unspliced antisense transcript that initiates in intron 1 of ST7, covers the first exon and terminates in the ST7 promoter region. Polyadenylated. Nb: it also overlaps exon 1 of ST7OT4. ST7OT2 - Spliced antisense transcripts. Multiple isoforms that share either some 5' or some 3' exons. Isoforms are between 900-1300 bp, with 4-6 exons and polyadenlyated. ST7OT3 - Spliced ~1kb transcript. Begins in intron 10 of ST7, shares exons 11-13 and sometimes 14 & 15 with ST7 plus has a number of unique exons. Some exons may also act as a alternative 3' end for ST7. ST7OT4 - Multiple spliced transcripts within the long first intron of ST7. However, Refseq ST7OT4 transcript may be protein coding. Transcription begins just ~200bp downstream from the end of first ST7 exon. | ||
===Function=== | ===Function=== | ||
Please input function information here. | Please input function information here. | ||
| + | |||
| + | ===Expression=== | ||
| + | ST7OT1 - abundantly expressed in testis, also expressed in cerebellum, skeletal muscle, uterus, cerebellum, spinal cord, fetal brain, and prostate. ST7OT2 - testis, fetal brain, cerebellum, mammary gland, fibroblasts. ST7OT3 - expression only detected in cerebellum. ST7OT4 - no expression detected. | ||
| + | |||
| + | ===Conservation=== | ||
| + | ST7OT1 - some conserved sequence with mouse, most of this is where ST7OT1 overlaps the first exon of ST7 however. ST7OT2 - 3' end of some isoforms shows some conservation with mouse. ST7OT3 - some conserved sequence, most of this is shared exons with ST7 though. ST7OT4 - sequence not conserved with mouse. | ||
| + | |||
| + | ===Misc=== | ||
| + | ST7OT1 - NCBI Gene ID: 93653. ST7OT2 - NCBI Gene ID: 93654. ST7OT3 - NCBI Gene ID: 93655. ST7OT4 - NCBI Gene ID: 338069 | ||
| + | |||
| + | ===Transcriptomic Nomeclature=== | ||
| + | Please input transcriptomic nomeclature information here. | ||
===Regulation=== | ===Regulation=== | ||
Please input regulation information here. | Please input regulation information here. | ||
| − | |||
| − | |||
| − | |||
===Allelic Information and Variation=== | ===Allelic Information and Variation=== | ||
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==References== | ==References== | ||
| − | + | [http://www.lncrnadb.org/st7ot/ Annotation originally sourced from lncRNAdb.] | |
{{basic| | {{basic| | ||
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sequence = <dnaseq>TACACTCCCAAGAGTGCCTTCGGGAACCCCTCTCCCCACTACCCAACCAGAGAGACAGCCCCACGCCCGGCAAGACGCAACTCCGGGCCACGGAGGGCGCCGCCCGGACAGCCCGGCCGGGTCAGGGGGCTTCGCCGCCGAGCACCCTCCGGCAGCCGCCCTCGGGCCTCCGCGGCCGGGCGGGAGGGCGCCTCCCCGACCACACTTCGGCCGCTTGGCACCCACAGCCGGGAGGGCGTGAGGAAGGACTCGGTCTAACTCCGGGGAACCCTCGGAGTTCCGGCGCAGACACCCGAGGGGGTGTCCTGGGAACTCCTTCGCCCGCGACACCCGTTCTTCTCCGTCTCCCGACCACCAGCGACGCAGCAGGGCGGCTGCCGGCCCGGCCCGGCCCGCCTTGCGGGCTGTGCGCGGCGCAGCTCTTCCTCCGCGGGGCCGTGAAGGCCACCGGCCGCCCCCGCGCGCCCAGCTGCCCGGCCCCGCCGCCTAAGCCGCCGCGTTGCTGGCGGGTAGCCGCGGGCCTCCGGTGCGCGGGCCCCGGCGCGTCCCCGAGCGCGCGCCTGGCCGCGGCCCCGCGCGAGTTGCACTAACTTTCCGGGGCGGGGGAGGGGTGGGCGCCGCGGGCCCGGCTCCCAGGCCTTACCTGTGCTCAAGTTGTCGTTGATTTTCAAAGGCACCCGCAGGATGTAGACCAGGAATAGCACGATGAAGAACCACACGGTCCACAGATACGTCCAAGACCAAACTATGCAGGACTTGAGCTGCTCCAGAAAGCCCGTGGCCGCTTCAGCCATGTTTCAGCGCTCCTCTCTGCTGCCGCGGCTCTTGGTGTCTGCCGGGATGATTCACCGGCCCGGAGGCGCAGCTCGCGCCGCCGCCGCCGCCGCGGCCCGGGCGCCCCCGGAGCCCGCCCGCCGCCGGGGACGCGGGCTCGGCGGGAAATCGCGCGGGCCGCGGGCGCGCCGGCTTTTCCTTCTCCAGCCTTATTGCTAACTCTCTAAAGGTCCCTACAAGTGGCTTTCGTGGAGCGATCACGTGGCCCCTGCCCCCTCGCGTTCTGGGTCCATTTATATTTATTATGCTAATATTTAGAAAGAGAAGGCCAAGTGGCGCGCCGAAGGAAACGCCTCAGGCAGTTACAACCCGCATAAGTTGAGCGTTTACCACACGCCAGGCGCTGCTCCACGATCCGTACAATCTCATTTAACCCCTGCAACAATTCCCCACTACGATCCTCTTTCTATAGGTAGGGAAACTGAGGCTCACAGCAGCTGCGTAGTTTACCTTAAGGTGGAACCAAAATTCAATTGCAGTGGTGTATTCTGGGGTCCGAGGTCTTAAACCCTACTCTGCTCCCTTATCAGGATTCAGGCTCAGGGAATGAATAAACCCGGGACAGCTAGGAGAAGGGAGGAGGTGCGCTCCTGTCGCCGGCTAGTAGGCCTGAAGATAAATCACTCTATTCAGCAAGATTTGGGTGGCAGATGCTATTTACCTTTGTTCTGTCTCTTTGAAGCAGCGCAGGGATTTTCCAGAGAAATCTTGACAGATGAATGTTTATCCTCCAGGTTTTTTGGTGATCAGAGGTCAAACTATTCTCAGCCTGTTTTTAATATAAACAATTCTCTGGGATAATTTTGACTGTGAAACGGCCACCTCTAACAGAAAGTCCATTTTAAACATTGTTTTGTTGTTTTTGTTTTGTTTTGACTGTGCTGAATAAAATGTTTCTTTTATTCTAAAATGTTTTCTCAGCTGAAATTTTCAAGTCTGTTTCTGTCCGTAAGTGATTTGACTTTCTATGTATTAGATGGTAATGAGGAAATTGCAGGTTTTCCAGTCTACATCTATTTTTAAAATTCTGAGCATAAAGAATATTTTATTATAAAAAAAAAAAAAAAAAAAAAA</dnaseq>| | sequence = <dnaseq>TACACTCCCAAGAGTGCCTTCGGGAACCCCTCTCCCCACTACCCAACCAGAGAGACAGCCCCACGCCCGGCAAGACGCAACTCCGGGCCACGGAGGGCGCCGCCCGGACAGCCCGGCCGGGTCAGGGGGCTTCGCCGCCGAGCACCCTCCGGCAGCCGCCCTCGGGCCTCCGCGGCCGGGCGGGAGGGCGCCTCCCCGACCACACTTCGGCCGCTTGGCACCCACAGCCGGGAGGGCGTGAGGAAGGACTCGGTCTAACTCCGGGGAACCCTCGGAGTTCCGGCGCAGACACCCGAGGGGGTGTCCTGGGAACTCCTTCGCCCGCGACACCCGTTCTTCTCCGTCTCCCGACCACCAGCGACGCAGCAGGGCGGCTGCCGGCCCGGCCCGGCCCGCCTTGCGGGCTGTGCGCGGCGCAGCTCTTCCTCCGCGGGGCCGTGAAGGCCACCGGCCGCCCCCGCGCGCCCAGCTGCCCGGCCCCGCCGCCTAAGCCGCCGCGTTGCTGGCGGGTAGCCGCGGGCCTCCGGTGCGCGGGCCCCGGCGCGTCCCCGAGCGCGCGCCTGGCCGCGGCCCCGCGCGAGTTGCACTAACTTTCCGGGGCGGGGGAGGGGTGGGCGCCGCGGGCCCGGCTCCCAGGCCTTACCTGTGCTCAAGTTGTCGTTGATTTTCAAAGGCACCCGCAGGATGTAGACCAGGAATAGCACGATGAAGAACCACACGGTCCACAGATACGTCCAAGACCAAACTATGCAGGACTTGAGCTGCTCCAGAAAGCCCGTGGCCGCTTCAGCCATGTTTCAGCGCTCCTCTCTGCTGCCGCGGCTCTTGGTGTCTGCCGGGATGATTCACCGGCCCGGAGGCGCAGCTCGCGCCGCCGCCGCCGCCGCGGCCCGGGCGCCCCCGGAGCCCGCCCGCCGCCGGGGACGCGGGCTCGGCGGGAAATCGCGCGGGCCGCGGGCGCGCCGGCTTTTCCTTCTCCAGCCTTATTGCTAACTCTCTAAAGGTCCCTACAAGTGGCTTTCGTGGAGCGATCACGTGGCCCCTGCCCCCTCGCGTTCTGGGTCCATTTATATTTATTATGCTAATATTTAGAAAGAGAAGGCCAAGTGGCGCGCCGAAGGAAACGCCTCAGGCAGTTACAACCCGCATAAGTTGAGCGTTTACCACACGCCAGGCGCTGCTCCACGATCCGTACAATCTCATTTAACCCCTGCAACAATTCCCCACTACGATCCTCTTTCTATAGGTAGGGAAACTGAGGCTCACAGCAGCTGCGTAGTTTACCTTAAGGTGGAACCAAAATTCAATTGCAGTGGTGTATTCTGGGGTCCGAGGTCTTAAACCCTACTCTGCTCCCTTATCAGGATTCAGGCTCAGGGAATGAATAAACCCGGGACAGCTAGGAGAAGGGAGGAGGTGCGCTCCTGTCGCCGGCTAGTAGGCCTGAAGATAAATCACTCTATTCAGCAAGATTTGGGTGGCAGATGCTATTTACCTTTGTTCTGTCTCTTTGAAGCAGCGCAGGGATTTTCCAGAGAAATCTTGACAGATGAATGTTTATCCTCCAGGTTTTTTGGTGATCAGAGGTCAAACTATTCTCAGCCTGTTTTTAATATAAACAATTCTCTGGGATAATTTTGACTGTGAAACGGCCACCTCTAACAGAAAGTCCATTTTAAACATTGTTTTGTTGTTTTTGTTTTGTTTTGACTGTGCTGAATAAAATGTTTCTTTTATTCTAAAATGTTTTCTCAGCTGAAATTTTCAAGTCTGTTTCTGTCCGTAAGTGATTTGACTTTCTATGTATTAGATGGTAATGAGGAAATTGCAGGTTTTCCAGTCTACATCTATTTTTAAAATTCTGAGCATAAAGAATATTTTATTATAAAAAAAAAAAAAAAAAAAAAA</dnaseq>| | ||
}} | }} | ||
| − | [[Category:Intergenic]] | + | [[Category:Intergenic]][[Category:NONHSAG048615]][[Category:Transcripts]] |
Latest revision as of 06:01, 26 August 2015
Please input one-sentence summary here.
Contents
Annotated Information
Name
ST7OT
Characteristics
Four noncoding RNAs from the RAY1/ST7 gene locus. Complex gene locus with a large number of coding and noncoding isoforms. ST7OT1 & 2 are antisense to ST7. ST7OT3 & 4 are on the sense strand. ST7OT1 - ~2kb unspliced antisense transcript that initiates in intron 1 of ST7, covers the first exon and terminates in the ST7 promoter region. Polyadenylated. Nb: it also overlaps exon 1 of ST7OT4. ST7OT2 - Spliced antisense transcripts. Multiple isoforms that share either some 5' or some 3' exons. Isoforms are between 900-1300 bp, with 4-6 exons and polyadenlyated. ST7OT3 - Spliced ~1kb transcript. Begins in intron 10 of ST7, shares exons 11-13 and sometimes 14 & 15 with ST7 plus has a number of unique exons. Some exons may also act as a alternative 3' end for ST7. ST7OT4 - Multiple spliced transcripts within the long first intron of ST7. However, Refseq ST7OT4 transcript may be protein coding. Transcription begins just ~200bp downstream from the end of first ST7 exon.
Function
Please input function information here.
Expression
ST7OT1 - abundantly expressed in testis, also expressed in cerebellum, skeletal muscle, uterus, cerebellum, spinal cord, fetal brain, and prostate. ST7OT2 - testis, fetal brain, cerebellum, mammary gland, fibroblasts. ST7OT3 - expression only detected in cerebellum. ST7OT4 - no expression detected.
Conservation
ST7OT1 - some conserved sequence with mouse, most of this is where ST7OT1 overlaps the first exon of ST7 however. ST7OT2 - 3' end of some isoforms shows some conservation with mouse. ST7OT3 - some conserved sequence, most of this is shared exons with ST7 though. ST7OT4 - sequence not conserved with mouse.
Misc
ST7OT1 - NCBI Gene ID: 93653. ST7OT2 - NCBI Gene ID: 93654. ST7OT3 - NCBI Gene ID: 93655. ST7OT4 - NCBI Gene ID: 338069
Transcriptomic Nomeclature
Please input transcriptomic nomeclature information here.
Regulation
Please input regulation information here.
Allelic Information and Variation
Please input allelic information and variation information here.
Evolution
Please input evolution information here.
You can also add sub-section(s) at will.
Labs working on this lncRNA
Please input related labs here.
References
Annotation originally sourced from lncRNAdb.
Basic Information
| Transcript ID |
NONHSAT122914 |
| Source |
NONCODE4.0 |
| Same with |
, |
| Classification |
intergenic |
| Length |
1908 nt |
| Genomic location |
chr7-:116592500..116594388 |
| Exon number |
1 |
| Exons |
116592500..116594388 |
| Genome context |
|
| Sequence |
000001 TACACTCCCA AGAGTGCCTT CGGGAACCCC TCTCCCCACT ACCCAACCAG AGAGACAGCC CCACGCCCGG CAAGACGCAA 000080
000081 CTCCGGGCCA CGGAGGGCGC CGCCCGGACA GCCCGGCCGG GTCAGGGGGC TTCGCCGCCG AGCACCCTCC GGCAGCCGCC 000160 000161 CTCGGGCCTC CGCGGCCGGG CGGGAGGGCG CCTCCCCGAC CACACTTCGG CCGCTTGGCA CCCACAGCCG GGAGGGCGTG 000240 000241 AGGAAGGACT CGGTCTAACT CCGGGGAACC CTCGGAGTTC CGGCGCAGAC ACCCGAGGGG GTGTCCTGGG AACTCCTTCG 000320 000321 CCCGCGACAC CCGTTCTTCT CCGTCTCCCG ACCACCAGCG ACGCAGCAGG GCGGCTGCCG GCCCGGCCCG GCCCGCCTTG 000400 000401 CGGGCTGTGC GCGGCGCAGC TCTTCCTCCG CGGGGCCGTG AAGGCCACCG GCCGCCCCCG CGCGCCCAGC TGCCCGGCCC 000480 000481 CGCCGCCTAA GCCGCCGCGT TGCTGGCGGG TAGCCGCGGG CCTCCGGTGC GCGGGCCCCG GCGCGTCCCC GAGCGCGCGC 000560 000561 CTGGCCGCGG CCCCGCGCGA GTTGCACTAA CTTTCCGGGG CGGGGGAGGG GTGGGCGCCG CGGGCCCGGC TCCCAGGCCT 000640 000641 TACCTGTGCT CAAGTTGTCG TTGATTTTCA AAGGCACCCG CAGGATGTAG ACCAGGAATA GCACGATGAA GAACCACACG 000720 000721 GTCCACAGAT ACGTCCAAGA CCAAACTATG CAGGACTTGA GCTGCTCCAG AAAGCCCGTG GCCGCTTCAG CCATGTTTCA 000800 000801 GCGCTCCTCT CTGCTGCCGC GGCTCTTGGT GTCTGCCGGG ATGATTCACC GGCCCGGAGG CGCAGCTCGC GCCGCCGCCG 000880 000881 CCGCCGCGGC CCGGGCGCCC CCGGAGCCCG CCCGCCGCCG GGGACGCGGG CTCGGCGGGA AATCGCGCGG GCCGCGGGCG 000960 000961 CGCCGGCTTT TCCTTCTCCA GCCTTATTGC TAACTCTCTA AAGGTCCCTA CAAGTGGCTT TCGTGGAGCG ATCACGTGGC 001040 001041 CCCTGCCCCC TCGCGTTCTG GGTCCATTTA TATTTATTAT GCTAATATTT AGAAAGAGAA GGCCAAGTGG CGCGCCGAAG 001120 001121 GAAACGCCTC AGGCAGTTAC AACCCGCATA AGTTGAGCGT TTACCACACG CCAGGCGCTG CTCCACGATC CGTACAATCT 001200 001201 CATTTAACCC CTGCAACAAT TCCCCACTAC GATCCTCTTT CTATAGGTAG GGAAACTGAG GCTCACAGCA GCTGCGTAGT 001280 001281 TTACCTTAAG GTGGAACCAA AATTCAATTG CAGTGGTGTA TTCTGGGGTC CGAGGTCTTA AACCCTACTC TGCTCCCTTA 001360 001361 TCAGGATTCA GGCTCAGGGA ATGAATAAAC CCGGGACAGC TAGGAGAAGG GAGGAGGTGC GCTCCTGTCG CCGGCTAGTA 001440 001441 GGCCTGAAGA TAAATCACTC TATTCAGCAA GATTTGGGTG GCAGATGCTA TTTACCTTTG TTCTGTCTCT TTGAAGCAGC 001520 001521 GCAGGGATTT TCCAGAGAAA TCTTGACAGA TGAATGTTTA TCCTCCAGGT TTTTTGGTGA TCAGAGGTCA AACTATTCTC 001600 001601 AGCCTGTTTT TAATATAAAC AATTCTCTGG GATAATTTTG ACTGTGAAAC GGCCACCTCT AACAGAAAGT CCATTTTAAA 001680 001681 CATTGTTTTG TTGTTTTTGT TTTGTTTTGA CTGTGCTGAA TAAAATGTTT CTTTTATTCT AAAATGTTTT CTCAGCTGAA 001760 001761 ATTTTCAAGT CTGTTTCTGT CCGTAAGTGA TTTGACTTTC TATGTATTAG ATGGTAATGA GGAAATTGCA GGTTTTCCAG 001840 001841 TCTACATCTA TTTTTAAAAT TCTGAGCATA AAGAATATTT TATTATAAAA AAAAAAAAAA AAAAAAAA |
