Difference between revisions of "Lnc-TCF24-2:3"

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==Annotated Information==
 
==Annotated Information==
 +
===Name===
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SNHG6: Small nucleolar RNA host gene 6
 +
 +
===Characteristics===
 +
Spliced transcript with U87 snoRNA in second intron. ~0.5kb transcript. Transcriptional start site has characteristics of 5' TOP gene family.
 +
 +
===Function===
 +
Unknown, however the authors point out that 5' TOP family genes are important for translation and that ribosomal associated SNHGs could be involved in this process as well.
 +
 +
===Expression===
 +
Broad expression in human and mouse tissues. Localises mostly to the cytoplasm. Human transcript found to show greater stability that SNHG1 in Hela cells [http://www.ncbi.nlm.nih.gov/pubmed/16226852 (Makarova (2005))]. Also found to be quite stable in human B cells with a half-life of 7 hr, while mouse Snhg6 was significantly less stable (half-life 2.2hrs in 3T3 cells), suggesting the transcripts may have different stabilities between species ([http://www.ncbi.nlm.nih.gov/pubmed/19561200 Friedel (2009)], [http://www.ncbi.nlm.nih.gov/pubmed/22406755 Clark (2012)]). Minority of SNHG6 associates with monosomes. Blocking translation led to a very modest increase in SNHG6 levels, in contrast to SNHG1 (which showed a large increase in transcript level) suggesting it is not very sensitive to nonsense mediated decay. This may help explain its increased stability.
 +
 +
===Conservation===
 +
Host gene sequence shows more conservation between species than other SNHG RNAs with conservation similar to levels of mRNA 3'UTRs. Conserved between human, mouse, rat and dog.
 +
 +
===Misc===
 +
Please input misc information here.
 +
 
===Transcriptomic Nomeclature===
 
===Transcriptomic Nomeclature===
 
Please input transcriptomic nomeclature information here.
 
Please input transcriptomic nomeclature information here.
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===Function===
 
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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/snhg6/ Annotation originally sourced from lncRNAdb.]
  
 
{{basic|
 
{{basic|
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sequence = <dnaseq>CCTTTCCCGCGCGACCGGCGAGGGAGGAAGAAGCGCGAAGAGCCGTTAGTCATGCCGGTGTGGTGGCGGCGGCGGAGACTGCGGGCCCGTAGCTGGGCTCTGCGAGGTGCAAGAAAGCCTTTGAGGTGAAGGTGTATGAAAGTCATCATAACAGATGTTTTCCAAAAACTTGTAGAAGGTTGTGAAAAAACTACTAGGATCACGCGGCATGTATTGAGCATATAGGTTGCTGTAGATGAATGTTCTTAGCTGTCATGTTTAAAAATACTTCTGCTTCGTTACCTCAAGTGTGGCATGCAGCATTTTGGAAGGAAAATTGAAGACGTGTTCAAGAAAACATGAACAGAAGCAAATGATGAAAATGAGCATTTTACTTGATGTTGATAACATCACAATAAATTATGGAGAAAAATACATATTTGGCTAACTTTTAATTGCTGAACAATAAAGTGTTTTCTTTTAAATCAACTCT</dnaseq>|
 
sequence = <dnaseq>CCTTTCCCGCGCGACCGGCGAGGGAGGAAGAAGCGCGAAGAGCCGTTAGTCATGCCGGTGTGGTGGCGGCGGCGGAGACTGCGGGCCCGTAGCTGGGCTCTGCGAGGTGCAAGAAAGCCTTTGAGGTGAAGGTGTATGAAAGTCATCATAACAGATGTTTTCCAAAAACTTGTAGAAGGTTGTGAAAAAACTACTAGGATCACGCGGCATGTATTGAGCATATAGGTTGCTGTAGATGAATGTTCTTAGCTGTCATGTTTAAAAATACTTCTGCTTCGTTACCTCAAGTGTGGCATGCAGCATTTTGGAAGGAAAATTGAAGACGTGTTCAAGAAAACATGAACAGAAGCAAATGATGAAAATGAGCATTTTACTTGATGTTGATAACATCACAATAAATTATGGAGAAAAATACATATTTGGCTAACTTTTAATTGCTGAACAATAAAGTGTTTTCTTTTAAATCAACTCT</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]]
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[[Category:Intergenic]][[Category:lnc-TCF24-2]][[Category:Transcripts]]
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{{lncrnadb|
 
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tID = lnc-TCF24-2:3|
 
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ltID = SNHG6|
 
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ann = <tab class=wikitable sep=tab head=top>
 
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Section Description
 
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ID SNHG6
 
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Characteristics Spliced transcript with U87 snoRNA in second intron. ~0.5kb transcript. Transcriptional start site has characteristics of 5' TOP gene family.
 
−
Expression Broad expression in human and mouse tissues. Localises mostly to the cytoplasm. Human transcript found to show greater stability that SNHG1 in Hela cells [http://www.ncbi.nlm.nih.gov/pubmed/16226852 (Makarova (2005))]. Also found to be quite stable in human B cells with a half-life of 7 hr, while mouse Snhg6 was significantly less stable (half-life 2.2hrs in 3T3 cells), suggesting the transcripts may have different stabilities between species ([http://www.ncbi.nlm.nih.gov/pubmed/19561200 Friedel (2009)], [http://www.ncbi.nlm.nih.gov/pubmed/22406755 Clark (2012)]). Minority of SNHG6 associates with monosomes. Blocking translation led to a very modest increase in SNHG6 levels, in contrast to SNHG1 (which showed a large increase in transcript level) suggesting it is not very sensitive to nonsense mediated decay. This may help explain its increased stability.
 
−
Function Unknown, however the authors point out that 5' TOP family genes are important for translation and that ribosomal associated SNHGs could be involved in this process as well.
 
−
Conservation Host gene sequence shows more conservation between species than other SNHG RNAs with conservation similar to levels of mRNA 3'UTRs. Conserved between human, mouse, rat and dog.
 
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Name SNHG6: Small nucleolar RNA host gene 6
 
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</tab>|
 
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}}
 

Latest revision as of 03:53, 26 August 2015

Please input one-sentence summary here.

Annotated Information

Name

SNHG6: Small nucleolar RNA host gene 6

Characteristics

Spliced transcript with U87 snoRNA in second intron. ~0.5kb transcript. Transcriptional start site has characteristics of 5' TOP gene family.

Function

Unknown, however the authors point out that 5' TOP family genes are important for translation and that ribosomal associated SNHGs could be involved in this process as well.

Expression

Broad expression in human and mouse tissues. Localises mostly to the cytoplasm. Human transcript found to show greater stability that SNHG1 in Hela cells (Makarova (2005)). Also found to be quite stable in human B cells with a half-life of 7 hr, while mouse Snhg6 was significantly less stable (half-life 2.2hrs in 3T3 cells), suggesting the transcripts may have different stabilities between species (Friedel (2009), Clark (2012)). Minority of SNHG6 associates with monosomes. Blocking translation led to a very modest increase in SNHG6 levels, in contrast to SNHG1 (which showed a large increase in transcript level) suggesting it is not very sensitive to nonsense mediated decay. This may help explain its increased stability.

Conservation

Host gene sequence shows more conservation between species than other SNHG RNAs with conservation similar to levels of mRNA 3'UTRs. Conserved between human, mouse, rat and dog.

Misc

Please input misc information here.

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

lnc-TCF24-2:3

Source

LNCipedia2.1

Same with

,

Classification

intergenic

Length

472 nt

Genomic location

chr8-:67834165..67837777

Exon number

4

Exons

67834165..67834349,67834559..67834627,67834849..67834960,67837672..67837777

Genome context

Sequence
000001 CCTTTCCCGC GCGACCGGCG AGGGAGGAAG AAGCGCGAAG AGCCGTTAGT CATGCCGGTG TGGTGGCGGC GGCGGAGACT 000080
000081 GCGGGCCCGT AGCTGGGCTC TGCGAGGTGC AAGAAAGCCT TTGAGGTGAA GGTGTATGAA AGTCATCATA ACAGATGTTT 000160
000161 TCCAAAAACT TGTAGAAGGT TGTGAAAAAA CTACTAGGAT CACGCGGCAT GTATTGAGCA TATAGGTTGC TGTAGATGAA 000240
000241 TGTTCTTAGC TGTCATGTTT AAAAATACTT CTGCTTCGTT ACCTCAAGTG TGGCATGCAG CATTTTGGAA GGAAAATTGA 000320
000321 AGACGTGTTC AAGAAAACAT GAACAGAAGC AAATGATGAA AATGAGCATT TTACTTGATG TTGATAACAT CACAATAAAT 000400
000401 TATGGAGAAA AATACATATT TGGCTAACTT TTAATTGCTG AACAATAAAG TGTTTTCTTT TAAATCAACT CT
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