Lnc-RASA1-3:23

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Annotated Information

Name

AK082072

Characteristics

Intergenic, 2 exon transcript in mouse, with HeK4me3 chromtain mark at 5' ((Chodroff 2010)).
Human ortholog is linc-POLR3G-8 ((Cabili 2011)). Human ortholog has a number of splice isoforms with 3 or more exons.

Function

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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” ((Chodroff 2010)).
Expressed in opossum and chicken embryonic brains showing spatio-temporal conservation of expression ((Chodroff 2010)).

Conservation

Highly conserved for a lincRNA 36.7% mouse transcript overlaps phastCons elements ((Chodroff 2010)).
Conserved in mammals and back to frog, although mouse exon 2 is not conserved in all orthologs ((Chodroff 2010)).
Opossum ortholog [GenBank:GU951678]. Frog and chicken ([GenBank: CX847574.1 and CR35248.1] respectively ((Chodroff 2010)).

Misc

Mouse transcript contains Evofold-predicted RNA secondary structure ((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 BC047059.

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

Annotation originally sourced from lncRNAdb.

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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