Difference between revisions of "NONHSAT054526"

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==Annotated Information==
 
==Annotated Information==
 +
===Name===
 +
SNHG5: Small nucleolar RNA host gene 5
 +
 +
===Characteristics===
 +
Contains U50 and U50-like snoRNAs in introns [http://www.ncbi.nlm.nih.gov/pubmed/10792466 (Tanaka (2000))]. Alternatively spliced transcript [http://www.ncbi.nlm.nih.gov/pubmed/10792466 (Tanaka (2000))]. Refseq isoform is ~0.5kb in humans. Transcriptional start site has characteristics of 5' TOP gene family [http://www.ncbi.nlm.nih.gov/pubmed/10792466 (Tanaka (2000))].
 +
 +
===Function===
 +
Please input function information here.
 +
 +
===Disease===
 +
lymphoma
 +
 +
===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 [http://www.ncbi.nlm.nih.gov/pubmed/22955988 (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  ([http://www.ncbi.nlm.nih.gov/pubmed/19561200 Friedel (2009)], [http://www.ncbi.nlm.nih.gov/pubmed/22406755 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 [http://www.ncbi.nlm.nih.gov/pubmed/17468437 (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 [http://www.ncbi.nlm.nih.gov/pubmed/17468437 (Tanaka-Fujita (2007))].
 +
 +
===Conservation===
 +
Please input conservation information here.
 +
 +
===Misc===
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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 [http://www.ncbi.nlm.nih.gov/pubmed/10792466 (Tanaka (2000))].
 +
 
===Transcriptomic Nomeclature===
 
===Transcriptomic Nomeclature===
 
Please input transcriptomic nomeclature information here.
 
Please input transcriptomic nomeclature information here.
  
−
===Function===
 
−
Please input function information here.
 
  
 
===Regulation===
 
===Regulation===
 
Please input regulation information here.
 
Please input regulation information here.
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−
===Expression===
 
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Please input expression information here.
 
  
 
===Allelic Information and Variation===
 
===Allelic Information and Variation===
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==References==
 
==References==
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Please input cited references here.
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[http://www.lncrnadb.org/snhg5/ Annotation originally sourced from lncRNAdb.]
  
 
{{basic|
 
{{basic|
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sequence = <dnaseq>CTTTTACGTCGGCCTTCGCGAGCGTCTGGGCGGGTGGTAGGAACAATGGCGCTGTCTTCAGTGGCACAGTGGAGCAGCTCTGAAGATGCAAAGATACACGAAAAAACTTCCAGAACATCTGGGAGAATATTTAATGGAAAATCGCTTGGTTAAAACCTGACACTTTTAACAGTGAACAGCGTTCTGAGTGTGGACGAGTAGCCAGTGAAGATAATGAATGTCGAATGTGACTGACTAGCAGCTTCATTTTGAATGAGGGTCGCTGTCTGCCCATTGATAGAGGCCAGATTGTCTTGGAAGTTCCAAAGTTGCAACGATTTCTGGCTAGTGCCACGAGGTTTACTTGACTGTTGTGTGAAAAGCTGATAAGAAAACCATCCAGAAAAAAGCTCTTCGTTTTACAAACATGAAAATAAAACATGTAATTTTGGATTATGTTCCTTTTTGTTATTACTTTTAAATAGGTCCTGAAATAACATGGGGAGCATTAAATGGAAAATCCACTAAAAAAAAAAAAAAAAAAA</dnaseq>|
 
sequence = <dnaseq>CTTTTACGTCGGCCTTCGCGAGCGTCTGGGCGGGTGGTAGGAACAATGGCGCTGTCTTCAGTGGCACAGTGGAGCAGCTCTGAAGATGCAAAGATACACGAAAAAACTTCCAGAACATCTGGGAGAATATTTAATGGAAAATCGCTTGGTTAAAACCTGACACTTTTAACAGTGAACAGCGTTCTGAGTGTGGACGAGTAGCCAGTGAAGATAATGAATGTCGAATGTGACTGACTAGCAGCTTCATTTTGAATGAGGGTCGCTGTCTGCCCATTGATAGAGGCCAGATTGTCTTGGAAGTTCCAAAGTTGCAACGATTTCTGGCTAGTGCCACGAGGTTTACTTGACTGTTGTGTGAAAAGCTGATAAGAAAACCATCCAGAAAAAAGCTCTTCGTTTTACAAACATGAAAATAAAACATGTAATTTTGGATTATGTTCCTTTTTGTTATTACTTTTAAATAGGTCCTGAAATAACATGGGGAGCATTAAATGGAAAATCCACTAAAAAAAAAAAAAAAAAAA</dnaseq>|
 
}}
 
}}
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[[Category:Intronic(S)]]
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[[Category:Intronic(S)]][[Category:NONHSAG022122]][[Category:Transcripts]][[Category:Transcripts]]
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{{lncrnadb|
 
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tID = NONHSAT054526|
 
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ltID = SNHG5|
 
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ann = <tab class=wikitable sep=tab head=top>
 
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Section Description
 
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ID SNHG5
 
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Characteristics Contains U50 and U50-like snoRNAs in introns [http://www.ncbi.nlm.nih.gov/pubmed/10792466 (Tanaka (2000))]. Alternatively spliced transcript [http://www.ncbi.nlm.nih.gov/pubmed/10792466 (Tanaka (2000))]. Refseq isoform is ~0.5kb in humans. Transcriptional start site has characteristics of 5' TOP gene family [http://www.ncbi.nlm.nih.gov/pubmed/10792466 (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 [http://www.ncbi.nlm.nih.gov/pubmed/22955988 (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  ([http://www.ncbi.nlm.nih.gov/pubmed/19561200 Friedel (2009)], [http://www.ncbi.nlm.nih.gov/pubmed/22406755 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 [http://www.ncbi.nlm.nih.gov/pubmed/17468437 (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 [http://www.ncbi.nlm.nih.gov/pubmed/17468437 (Tanaka-Fujita (2007))].
 
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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 [http://www.ncbi.nlm.nih.gov/pubmed/10792466 (Tanaka (2000))].
 
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Name SNHG5: Small nucleolar RNA host gene 5
 
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</tab>|
 
−
}}
 

Latest revision as of 14:25, 1 July 2016

Please input one-sentence summary here.

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

Please input function information here.

Disease

lymphoma

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

Please input conservation information here.

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

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

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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