Difference between revisions of "NONHSAT001953"

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==Annotated Information==
 
==Annotated Information==
 +
===Name===
 +
SNHG3: Small nucleolar RNA host gene 3
 +
 +
===Characteristics===
 +
Upstream from the RCC1 protein coding gene. Multiple SNHG3 splice isoforms exist, minority join RCC1, majority do not. Isoforms range from ~0.9kb to ~2.6kb in human.
 +
 +
Contain U17a and U17b snoRNAs in introns.
 +
 +
SNHG3 contains a number of exonic Alu elements
 +
 +
Transcriptional start site has characteristics of 5' TOP gene family.
 +
 +
===Function===
 +
Involved in maintaining pluripotency in ESCs [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))].
 +
 +
Knockdown in mECSs lead to down-regulation of Nanog, Sox2, Klf4 and Oct4 expression as well as changes to ESC morphology [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))].
 +
 +
Snhg3 was found to interact with a number of chromatin binding proteins/complexes in mESCs including PRC1, PRC2, JARID1B and SUV39H1, with the general pattern being interaction with repressors of gene expression [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))].
 +
 +
===Expression===
 +
Localised to cytoplasm. Unlike SNHG1 it was not stabilised by translation inhibitors or associated with translating ribosomes and was unaffected by translation inhibitors.
 +
 +
Identified as expressed in mouse embryonic stem cells [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))].
 +
 +
Transcript found to be unstable with a half-life <2 hr in mouse N2A (neuroblastoma) cells and human B cells ([http://www.ncbi.nlm.nih.gov/pubmed/19561200 Friedel (2009)], [http://www.ncbi.nlm.nih.gov/pubmed/22406755 Clark (2012)]).
 +
 +
===Conservation===
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Not highly conserved, ~40-50% identity between mouse and human exons.
 +
 +
===Misc===
 +
Please input misc information here.
 +
 
===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.
 
===Expression===
 
Please input expression information here.
 
  
 
===Allelic Information and Variation===
 
===Allelic Information and Variation===
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}}
 
}}
 
[[Category:Intergenic]]
 
[[Category:Intergenic]]
 
{{lncrnadb|
 
tID = NONHSAT001953|
 
ltID = SNHG3|
 
ann = <tab class=wikitable sep=tab head=top>
 
Section Description
 
ID SNHG3
 
Characteristics Upstream from the RCC1 protein coding gene. Multiple SNHG3 splice isoforms exist, minority join RCC1, majority do not. Isoforms range from ~0.9kb to ~2.6kb in human. Contain U17a and U17b snoRNAs in introns. SNHG3 contains a number of exonic Alu elements. Transcriptional start site has characteristics of 5' TOP gene family.
 
Expression Localised to cytoplasm. Unlike SNHG1 it was not stabilised by translation inhibitors or associated with translating ribosomes and was unaffected by translation inhibitors. Identified as expressed in mouse embryonic stem cells [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))]. Transcript found to be unstable with a half-life <2 hr in mouse N2A (neuroblastoma) cells and human B cells ([http://www.ncbi.nlm.nih.gov/pubmed/19561200 Friedel (2009)], [http://www.ncbi.nlm.nih.gov/pubmed/22406755 Clark (2012)]).
 
Function Involved in maintaining pluripotency in ESCs [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))]. Knockdown in mECSs lead to down-regulation of Nanog, Sox2, Klf4 and Oct4 expression as well as changes to ESC morphology [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))]. Snhg3 was found to interact with a number of chromatin binding proteins/complexes in mESCs including PRC1, PRC2, JARID1B and SUV39H1, with the general pattern being interaction with repressors of gene expression [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))].
 
Conservation Not highly conserved, ~40-50% identity between mouse and human exons.
 
Name SNHG3: Small nucleolar RNA host gene 3
 
</tab>|
 
}}
 

Revision as of 07:08, 10 October 2014

Please input one-sentence summary here.

Annotated Information

Name

SNHG3: Small nucleolar RNA host gene 3

Characteristics

Upstream from the RCC1 protein coding gene. Multiple SNHG3 splice isoforms exist, minority join RCC1, majority do not. Isoforms range from ~0.9kb to ~2.6kb in human.

Contain U17a and U17b snoRNAs in introns.

SNHG3 contains a number of exonic Alu elements

Transcriptional start site has characteristics of 5' TOP gene family.

Function

Involved in maintaining pluripotency in ESCs (Guttman (2011)).

Knockdown in mECSs lead to down-regulation of Nanog, Sox2, Klf4 and Oct4 expression as well as changes to ESC morphology (Guttman (2011)).

Snhg3 was found to interact with a number of chromatin binding proteins/complexes in mESCs including PRC1, PRC2, JARID1B and SUV39H1, with the general pattern being interaction with repressors of gene expression (Guttman (2011)).

Expression

Localised to cytoplasm. Unlike SNHG1 it was not stabilised by translation inhibitors or associated with translating ribosomes and was unaffected by translation inhibitors.

Identified as expressed in mouse embryonic stem cells (Guttman (2011)).

Transcript found to be unstable with a half-life <2 hr in mouse N2A (neuroblastoma) cells and human B cells (Friedel (2009), Clark (2012)).

Conservation

Not highly conserved, ~40-50% identity between mouse and human exons.

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

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Basic Information

Transcript ID

NONHSAT001953

Source

NONCODE4.0

Same with

,

Classification

intergenic

Length

2346 nt

Genomic location

chr1+:28832455..28837404

Exon number

4

Exons

28832455..28832596,28832732..28832839,28834640..28834672,28835342..28837404

Genome context

Sequence
000001 GATTCTCTAA CTGCGCATGC TTCTGCGCAC GCGCAATAGA CATTCCAGGA CTTCCGGGCA CTTCGTAAGG TTTAAAAAGG 000080
000081 ATGCTTCGCG TTTTCTCTCT CCTTTTTGGA GACAGATTCG CAGTGGTCGC TTCTTCTCCT TGACGGAGTC GGTTTGTCAC 000160
000161 TCAGGCTGGA CTGCAGTGCT CGTTGCAACC TCCGCCTGCC GGGTTCAAGC GATTCTCGTG CCTCAGCCTC TCCAGCAGCT 000240
000241 GGGATTACAG GATTTGTTAA GGATTCCAAG TAACTCTTAT TTGGAGAGAA GACGATCTGC ACTTCGCATT TTGGCATTGA 000320
000321 CATTTAATTT TAGGGTCCTT TATATAGAAG GGAGAGTAGG TAAACTGATT TTTTTTTTTA ACAGGGAGGG TTTGACAATC 000400
000401 TTTGGCAGAC TTGGAGCAAA AGATTGAGGT GCATTTCATG CCTCCTTTTG AGAGTCTTGC TCTGTCGCCC AGGCTGTAGT 000480
000481 GCAGTGGCGC AATCTTGGCT GCAACCTCAG CCTCCCAAGT AGCTGGGATT ACAAACATAA GCCACCACGC CCAGCCCTCA 000560
000561 TACCTCTTTT AAAAGTCGAC CTGTTTTGCA GAAAGTCTGC TGTTTTTGTA CTAAAGGCTT TGGAATTTGG CATTTAGCTA 000640
000641 GGAATGCACA TTCTTTCACC TCATTCATAC TTTAAGAACC ACAGAAGTGA CTCTGCTTGG CCAGAAGGCA CACTGTGTTG 000720
000721 GTGGTTATAT TAAAAGTCCT TGAGTATTTT GCTTTTCATG ATCTTGCTCA CTGCAACTTC CGCCTCCCAG GTTCAGGCGA 000800
000801 TTCTCCTGCC TCAGCCTCCC AAGTAGCTGC GACTACAGGC GTGTAGCACC ACACCTGGCT AATTTTTGTA TTTTTAGTAG 000880
000881 AGATGAGGTT TCACCATATT GGCCAGGCTG TTCTCAACTC CTGACCTCGT GATCCGCCCA CCTCAGCCTC CTAAAGTGCT 000960
000961 GGGATTACAG CTGTGAGCCA CCCTGCCCGG CCACTTTTGT ATGATTTCTA ATGTATTTGT AATTTACCTA ACAAATTGCC 001040
001041 TAATCTGCTA TGTTAATGTA TTTATGAATT AAAATAAATA CGACTGCATG TTTGTGGTTC ATTTTTGTGG AGGTGGCTGT 001120
001121 GGTGACATCA GCCAAGAATC TGAATGGTAC TGTTGAAGGA AACTAGCATG ATAGCTTCAG TTCTAAAGGC CCTGAAACCT 001200
001201 AGTCTCAGGT GGGTCCCCCT TGGGTTCACT TTATATTGGC AGTTTATTGG GAAAATGGAT ATTAGGTCCT GACCAATAGG 001280
001281 ACCGTAAGTC TGGGTTGAGT GCAAGATGAG TTAGACCGAT TCTTTAGCTT CCTGCAGTGT AGTGGAGGAA AAATCGATGG 001360
001361 TAGCAACGGG AGGTTGTATC CCTAGCTGAT GAGTTGTATG AGCCTCTACT ACCTGGCGCA CCTCCGCCTG AAGATTGCCA 001440
001441 GAATTGCTTG CCTCATGACG TGAGTCACAA TGGAAACTTT GTCAAGCCCC CTGCACTGGC TGCCAACATA AATGTTCAGT 001520
001521 ACCCTGAAGG ATGGGACTGA AGGGGGATCA TCTAGAAGGT AAAGTTACCT ACTGGCATAG GGGAGGTGGG ACAGCCGTTA 001600
001601 AGCCATTTGG AACTTGATGG AGACAGGTTT GAGGGAGGTG GGTGAGATTG GAGTTTGGTG GACTGTAGAG CTTGCTTGCC 001680
001681 AAGGTGTTGA GGTCAGGGTT GGTTTGAGAA TGGAAGCTAG TTACTAGCTA TGATTGTGGG GGAACACAGC TTGATTTTTC 001760
001761 TTACAAGCTA AGAGGAGTGA GGCAGTGTTT AAGAGGGCAT GTTAAATGCA GCCAGGCTTG GTGGCTCACA CCCGTAATCC 001840
001841 CAGCACTTAG GCTAAGGCAG GCGGATCACA ACATCTAGAG ATCCTGGCCA ACGCGGTGAA ACCCTGTCTG TACTAAAAAT 001920
001921 ACAAAATAAC TGGGCATGGT GGTGTGCACC TGTGGGAGGC TGAGGCAGAA TTGCTGGAAC CCGGGAGATG GAGGTTGTAC 002000
002001 TGAGCTGAGA CCTTGCCACT GCGCTCCAGC CTGGTGACAG AGTTAAGTCT CAAAAAAAAG GCATCTTCCT AAAGCAATTG 002080
002081 TATTTGTGCT TACCTGTGCC AGGCACTGTT CTAGGTAAGC ACTAAGTGGG CTTTAATACA GCATATTCCA ATGGGGAATC 002160
002161 CCAGGAACCA AAAGACTAAT TGTCCAAGTC CACAACTAGA AGTGGCACCT CTGCAGAAAC AAGCATCAAA TTCCCTGCTC 002240
002241 AGGAAGAAGC CAGATGAGTC AGCCCCATTC GTCTGTATGC CCAGTCCCAT CCGTGTCCTG CTGTAACTAC ATAGATCTCA 002320
002321 CCTGAGTAAA GTGATTTTTT TCTGAA
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Predicted Small Protein

Name NONHSAT001953_smProtein_2150:2305
Length 52
Molecular weight 5630.549
Aromaticity 0.0196078431373
Instability index 77.8235294118
Isoelectric point 9.69427490234
Runs 9
Runs residual 0.0222286934576
Runs probability 0.0374688413904
Amino acid sequence MGNPRNQKTNCPSPQLEVAPLQKQASNSLLRKKPDESAPFVCMPSPIRVLL
Secondary structure LLLLLLLLLLLLLLLLLLLLHHHHHLHHHHLLLLLLLLLEEELLLLEEEEL
PRMN -
PiMo -