Difference between revisions of "NONHSAT054526"
(Created page with "Please input one-sentence summary here.
==Annotated Information==
===Transcriptomic Nomeclature===
Please input transcriptomic nomeclature information here.
===Functio...") |
|||
| (6 intermediate revisions by 6 users not shown) | |||
| Line 2: | Line 2: | ||
==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=== | ||
| + | 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. | ||
| − | |||
| − | |||
===Regulation=== | ===Regulation=== | ||
Please input regulation information here. | Please input regulation information here. | ||
| − | |||
| − | |||
| − | |||
===Allelic Information and Variation=== | ===Allelic Information and Variation=== | ||
| Line 26: | Line 43: | ||
==References== | ==References== | ||
| − | + | [http://www.lncrnadb.org/snhg5/ Annotation originally sourced from lncRNAdb.] | |
{{basic| | {{basic| | ||
| Line 42: | Line 59: | ||
sequence = <dnaseq>CTTTTACGTCGGCCTTCGCGAGCGTCTGGGCGGGTGGTAGGAACAATGGCGCTGTCTTCAGTGGCACAGTGGAGCAGCTCTGAAGATGCAAAGATACACGAAAAAACTTCCAGAACATCTGGGAGAATATTTAATGGAAAATCGCTTGGTTAAAACCTGACACTTTTAACAGTGAACAGCGTTCTGAGTGTGGACGAGTAGCCAGTGAAGATAATGAATGTCGAATGTGACTGACTAGCAGCTTCATTTTGAATGAGGGTCGCTGTCTGCCCATTGATAGAGGCCAGATTGTCTTGGAAGTTCCAAAGTTGCAACGATTTCTGGCTAGTGCCACGAGGTTTACTTGACTGTTGTGTGAAAAGCTGATAAGAAAACCATCCAGAAAAAAGCTCTTCGTTTTACAAACATGAAAATAAAACATGTAATTTTGGATTATGTTCCTTTTTGTTATTACTTTTAAATAGGTCCTGAAATAACATGGGGAGCATTAAATGGAAAATCCACTAAAAAAAAAAAAAAAAAAA</dnaseq>| | sequence = <dnaseq>CTTTTACGTCGGCCTTCGCGAGCGTCTGGGCGGGTGGTAGGAACAATGGCGCTGTCTTCAGTGGCACAGTGGAGCAGCTCTGAAGATGCAAAGATACACGAAAAAACTTCCAGAACATCTGGGAGAATATTTAATGGAAAATCGCTTGGTTAAAACCTGACACTTTTAACAGTGAACAGCGTTCTGAGTGTGGACGAGTAGCCAGTGAAGATAATGAATGTCGAATGTGACTGACTAGCAGCTTCATTTTGAATGAGGGTCGCTGTCTGCCCATTGATAGAGGCCAGATTGTCTTGGAAGTTCCAAAGTTGCAACGATTTCTGGCTAGTGCCACGAGGTTTACTTGACTGTTGTGTGAAAAGCTGATAAGAAAACCATCCAGAAAAAAGCTCTTCGTTTTACAAACATGAAAATAAAACATGTAATTTTGGATTATGTTCCTTTTTGTTATTACTTTTAAATAGGTCCTGAAATAACATGGGGAGCATTAAATGGAAAATCCACTAAAAAAAAAAAAAAAAAAA</dnaseq>| | ||
}} | }} | ||
| − | [[Category:Intronic(S)]] | + | [[Category:Intronic(S)]][[Category:NONHSAG022122]][[Category:Transcripts]][[Category:Transcripts]] |
Latest revision as of 14:25, 1 July 2016
Please input one-sentence summary here.
Contents
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 |
