NONHSAT054526
Revision as of 12:07, 6 October 2014 by 111.204.253.116 (talk)
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Contents
Annotated Information
Transcriptomic Nomeclature
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Function
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Regulation
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Expression
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Allelic Information and Variation
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Evolution
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Labs working on this lncRNA
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References
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Basic Information
Transcript ID |
NONHSAT054526 |
Source |
NONCODE4.0 |
Same with |
, |
Classification |
intronic(S) |
Length |
524 nt |
Genomic location |
chr17-:47416677..47417192 |
Exon number |
1 |
Exons |
47416677..47417192 |
Genome context |
|
Sequence |
000001 CTTTTACGTC GGCCTTCGCG AGCGTCTGGG CGGGTGGTAG GAACAATGGC GCTGTCTTCA GTGGCACAGT GGAGCAGCTC 000080
000081 TGAAGATGCA AAGATACACG AAAAAACTTC CAGAACATCT GGGAGAATAT TTAATGGAAA ATCGCTTGGT TAAAACCTGA 000160 000161 CACTTTTAAC AGTGAACAGC GTTCTGAGTG TGGACGAGTA GCCAGTGAAG ATAATGAATG TCGAATGTGA CTGACTAGCA 000240 000241 GCTTCATTTT GAATGAGGGT CGCTGTCTGC CCATTGATAG AGGCCAGATT GTCTTGGAAG TTCCAAAGTT GCAACGATTT 000320 000321 CTGGCTAGTG CCACGAGGTT TACTTGACTG TTGTGTGAAA AGCTGATAAG AAAACCATCC AGAAAAAAGC TCTTCGTTTT 000400 000401 ACAAACATGA AAATAAAACA TGTAATTTTG GATTATGTTC CTTTTTGTTA TTACTTTTAA ATAGGTCCTG AAATAACATG 000480 000481 GGGAGCATTA AATGGAAAAT CCACTAAAAA AAAAAAAAAA AAAA |
Annotation (From lncRNAdb)
Section | Description |
---|---|
ID | SNHG5 |
Characteristics | Contains U50 and U50-like snoRNAs in introns (Tanaka (2000)). Alternatively spliced transcript (Tanaka (2000)). Refseq isoform is ~0.5kb in humans. Transcriptional start site has characteristics of 5' TOP gene family (Tanaka (2000)). |
Expression | Broadly expressed in human adult tissues. Identified as enriched in the cytoplasm of human GM12878, HepG2, HUVEC and K562 cells bu nuclear enriched in HeLaS3 (Derrien (2012)). RNA is unstable with a half-life <2 hr in mouse N2A (neuroblastoma) and 3T3 cells and a half-life ~2 hr in human B cells (Friedel (2009), Clark (2012)). |
Conservation | Mouse has two transcripts at syntenic loci which are separated by several hundred kb and contain U50. Some sequence similarity is found between then so it is likely they share a common ancestor (Tanaka-Fujita (2007)). Comparing mouse and human host transcripts revealed they were "dissimilar". It was hypothesized that the host transcripts share a common ancestor but there has been little selection for maintaining the sequence the host gene exons (Tanaka-Fujita (2007)). |
Misc | SNHG5 forms a novel translocation breakpoint with Bcl6 in a diffuse large B-cell (DLB) lymphoma, although it is unclear if SNHG5 contributed to malignancy (Tanaka (2000)). |
Name | SNHG5: Small nucleolar RNA host gene 5 |