Lnc-RASA1-3:23

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Annotated Information

Transcriptomic Nomeclature

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Function

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Regulation

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Expression

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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	lnc-RASA1-3:23
Source	LNCipedia2.1
Same with	NONHSAT102650
Classification	intergenic
Length	953 nt
Genomic location	chr5+:87686219..87732860
Exon number	3
Exons	87686219..87686278,87705890..87706011,87732090..87732860
Genome context
Sequence	000001 CCAGACACCA CCGAGAGACA CAGGGCTTTT TAGCGTTCAC TGTATTTTCA CTTCCACCGG ATCCAATGTG ATAATTTATG 000080 000081 TGAAATCTTT CTGCAAACTA TACAGTATGA TAAAAATATA AGGTAGTTTC ACTGGAAACA ACAGAAGACT AGAAGCTGAT 000160 000161 GTGACGTGGC AATATCAACC AGGAATACCC ATCTCGAGTT CTGGATATGT GCTCTGAGAA GGTGCCCATG TCACCGACCA 000240 000241 CACTGGAGGC CAATGCAGAT ACTGGGGGAA GGTTCCATGG TAGCTAAGTG TGGACAAGCT AATCACTGAA GTTCCCTGAT 000320 000321 GCAGAGTTGA TAATCTCTCT AGAGTTGGAT GAAAGACTGT GCTGCCTTGA AGCTCTGAGA GATGCCATGC CAATTCAAGG 000400 000401 CAGGGTCTTT ATTGTTGAAA CTCTTGCGTA ATGACATCTT TATTCAGGTG AAAATACAGG ATGAATTTCA ACTATATGAT 000480 000481 ATTGTTTATG TTCCTCAGAC ATGTTATTTG TCTTTACAAA GATTGGTTTC AATAAACTGT GTGACTGATA TTAAATAAAC 000560 000561 ATGGAATTTT ACACATTCAT AATATTTGGT TTCTTGTGAT TTTGATGAAC TATACTTTCA AGCATTGTCA GTTCATCCTC 000640 000641 ATTTACAAGG AAACATTTGC TGTAGCAGAG TGATGTAGTG ACTTGCTTTA CTTAAGATAA GTCAACTTTT CTATTCAATG 000720 000721 TTTAATGTGA AACTGACTTA AAAATTTTCT TTTAGGCCAC ATTTACATTT CTGTTTGTAT AACATGCATT ATACTATTTT 000800 000801 AACTTAATAC TATGGCTATA TAAACCAAAG ACATCCTAAT TCTGTTTTTA ATTTATTGTT TTGCAAGATA AATAATTTTT 000880 000881 AATGCACTAA TGAAGCTAAG GAGTTCATAT TAAAAGACAT GTTATATGAC CTACTGAAGT TGAGCTATGG AAA

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Annotation (From lncRNAdb)

[lnc-RASA1-3:23]

Section	Description
ID	AK082072
Characteristics	Intergenic, 2 exon transcript in mouse, with HeK4me3 chromtain mark at 5' ([www.ncbi.nlm.nih.gov/pubmed/20624288 (Chodroff 2010)]). Human ortholog is linc-POLR3G-8 ([www.ncbi.nlm.nih.gov/pubmed/21890647 (Cabili 2011)]). Human ortholog has a number of splice isoforms with 3 or more exons.
Expression	Expressed in specific regions of embryonic and post-natal mouse brain (see Chodroff for details) including the rostal migratory stream at P3 with a “potential association with inhibitory GABAergic neurons” ([www.ncbi.nlm.nih.gov/pubmed/20624288 (Chodroff 2010)]). Expressed in opossum and chicken embryonic brains showing spatio-temporal conservation of expression ([www.ncbi.nlm.nih.gov/pubmed/20624288 (Chodroff 2010)]).
Conservation	Highly conserved for a lincRNA 36.7% mouse transcript overlaps phastCons elements ([www.ncbi.nlm.nih.gov/pubmed/20624288 (Chodroff 2010)]). Conserved in mammals and back to frog, although mouse exon 2 is not conserved in all orthologs ([www.ncbi.nlm.nih.gov/pubmed/20624288 (Chodroff 2010)]). Opossum ortholog [GenBank:GU951678]. Frog and chicken ([GenBank: CX847574.1 and CR35248.1] respectively ([www.ncbi.nlm.nih.gov/pubmed/20624288 (Chodroff 2010)]).
Misc	Mouse transcript contains Evofold-predicted RNA secondary structure ([www.ncbi.nlm.nih.gov/pubmed/20624288 (Chodroff 2010)]). LncRNA transcripts in human from bidirectional promoter with TMEM161B (over 50kb upstream from linc-POLR3G-8 start site) can also share exons 2 and/or 3. See [www.ncbi.nlm.nih.gov/nuccore/BC047059 BC047059].

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