NONHSAT054526

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Annotated Information

Name

SNHG5: Small nucleolar RNA host gene 5

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)).

Function

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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)).

Conservation

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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)).

Transcriptomic Nomeclature

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Regulation

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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

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