NONHSAT001953

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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

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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	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 CTA