Lnc-BIRC7-2:1

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Annotated Information

Name

HAR1A

Characteristics

~2.8kb, spliced 2 exon transcript. Contains a 'human accelerated region' (HAR). Overlaps with an antisense noncoding RNA, HAR1B [(Pollard (2006))]
Conserved HAR1 sequence (common to both HAR1A and HAR1B) forms a secondary structure which is highly conserved (Pollard (2006)) but has undergone changes from a hairpin structure in chimps to a cloverleaf structure in humans (Beniaminov (2008)).

Function

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Expression

Expressed in adult brain and during cortical development (Pollard (2006))
Expressed in Cajal-Retzius neurons in the neocortex during early to mid-gestation (7-9 to 17-19 weeks) in humans and macaques (Pollard (2006))
During mid-gestation expressed in developing hippocampus, dentate gyrus and cerebellar cortex in human. Expression was found in adult brain, ovary and testis [(Pollard (2006))]
Repressed transcriptionally by REST, which causes repression of HAR1A in the striatum of Huntington's disease patients (Johnson (2010))
The overlapping antisense RNA (HAR1B) is also expressed in adult brain (Pollard (2006))
In mouse, locus is expressed during embryonic development (peak at E15) and in adults it is specifically expressed in the brain (Pollard (2006)).

Conservation

Contains a 'human accelerated region', which is a sequence highly conserved in amniotes (negative selection) but which has evolved rapidly in the human lineage (positive selection) since the divergence of humans and chimpanzees from the last common ancestor (18 bases out of 118 are different between human and chimpanzee but only 2 differences between chimpanzee and chicken) (Pollard (2006)).. HAR1A has orthologues in a number of closely mammals but in mouse and more distantly related species only the HAR1 sequence is conserved (Pollard (2006)).

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	lnc-BIRC7-2:1
Source	LNCipedia2.1
Same with	NONHSAT080828
Classification	intergenic
Length	2794 nt
Genomic location	chr20+:61732644..61735737
Exon number	2
Exons	61732644..61734606,61734907..61735737
Genome context
Sequence	000001 GGGAGTGTTG AGGGGGCCTG AAGGGTTCCG CTCCTCCCAC CCAGGGAACC GCCATGCCAC TAGTGGGCTG TCCTGGAGAC 000080 000081 TCGGGGAGAA AGCACACAGG CTGTCGGGAA AGGTGGGTCG CAGGCGGGCA GGGCAGCCCT GCTGTACTGA TGGGCAGGCG 000160 000161 CTGGGTGGGT GGAAGGCAAA GCCATCAGGT CATCCCCCTC TCTGTCCCTG CATTGGGCCA ACCAGGTGTG TCAGGAGGAT 000240 000241 ATTTGACCAT TCCTGAGAGG CACATTCTCT CTCTCTCTCT CTCTCTCCCT CTCTCTCTCT CCCTCTCTCT CTCCCTCTCT 000320 000321 CCCTCTCTCT CCCTCTCTCT CCCTCTCTCT CCCTCTCCCT CTCTCTCTCC CTCTCCCTCT CTCCCCCCTC CCTCTCCCTC 000400 000401 CCTCTCCCCC TCTCCCTCTC CCTCTCTCCC CCTCCCTCTC TCTCCCTCTC TCTCCCTCTC TCTCCCCCTC TCTCTCCCTC 000480 000481 CTCTCTCTGT CACACACATT TGCACATCCT GCAGTGTGAA TGGAGTATGA ATGTGTGTGG TAGGCGACAG CTGTGTGTGT 000560 000561 ACGTCCGGGT GCGTGTGTGC GTGTGTACAT GTGAGCGTGT GTGCACGTGA GTTAGAGCCT GAGTGTCCCC TGCGTGGGTT 000640 000641 AGTGTGTGCG CCCGCCCGGT GCCCTCCGTC TTGGGAGTCT GGGCTGCTGC TCCGCGGGCT CTGGAGCCGG CGCTCCCCAC 000720 000721 GAGCCCGGAC TCTCCGCCGC GCCCGGGAGC TGCGCAATCG GCTGCTAAGA CGCCGGCGCC ACCGGCTGGG CCCTGTTCTC 000800 000801 CCCTCTCTTT TCTACAGTCT TACCCGCAGC TGACAGGGTT CGAAAGAGCA TGAAACGGAG GAGACGTTAC AGCAACGTGT 000880 000881 CAGCTGAAAT GATGGGCGTA GACGCACGTC AGCGGCGGAA ATGGTTTCTA TCAAAATGAA AGTGTTTAGA GATTTTCCTC 000960 000961 AAGTTTCAAA TGAGGCGAAT CCCGTTTTCC GCGATGCTGC AGCGCGCGGG TTTTAACCGC AGGGTCACGC GGAACGCCGC 001040 001041 GCCGCGCGAC TGTGCCTCGG TCTCTGCGCC CGGCTCTCCC TCCGGTCCGC AAGAGGAGGA AGGCCCGCGG CGTGCCGAGG 001120 001121 TCAGCGGCGC GGAGCCACCA GGCGAGACGG TCACGGACGC CTGAACCGAG GTCACCGAGG CCACGGGGCC GGGAGGCCCT 001200 001201 CAGCAGAGCC CGGGGGCTCC GCACCTCAAG GCCGGCCAGG AAGAAACAGC AGCAGGAGCC CAGGGCGCCC CGGGGAGCCC 001280 001281 CCGACACGCG GGCCGAGCGC CCAGAGCGGC CCAGGCCCTC GCGAGGAGAC CGGCCTCCCC AGGGCGGGGC TTCCGACTCG 001360 001361 GGCGCCCGTG AGCCCCGGAG GCGGCGCGAA GGGGCAGAGT CCGCGTTTCT AACCAGCCCC CGGGTGGGCG GTGGCCCGCG 001440 001441 CGGCACGGTG GGCGCGAGCG CCGTGGGCTG GGGCCGGCCT GGGCTTTCAG GGCGAGGGCT TTCCGCGCCG GCCCCAGCCC 001520 001521 ACCCGGCCCC GCTGCGCGCC CCTCACGCTG CAGCCTGGGA ACCTGGGCCG GGAGCTGCGG GCCGCTCCGG GGAAGCGGGC 001600 001601 CTGACCTCCC CTCCCCACCG CCGCCCCTGC GGTGAGATCC TGCCTGCCGG GGCGCAGGGG CCCGCGGTTG GGCTCCGGGA 001680 001681 GACGGAAGAG GCCCCACAGC TCGGGCCCCA CGCAGTGGAC GCTGCCACTT AATTTTGGCG TAATTGATGT CAAGGCGGGT 001760 001761 GCCCGGGCCC CCAGTGAAAT GCCTCATGAA CTCGCTGCGA GGAACGGCGC TCCACGCGGT GCACGGTGGC CAATCAGAGC 001840 001841 TGCCGCTTCT GATGGAGGCT GAGCCGGCTG GGGAGGCGTC TTGGCCAAGA ACCAGCCCCA GCCTCGCTCA GGGCCCCAAC 001920 001921 CCGCAGACCA TGTAATTAAG CTGCGTTCTG CAGCCAGGGC AAGAGTCTCA GCTCTGAACA TCTTCCCGCA CCTCTGAGGA 002000 002001 GCCAGGCCTG GAAACCCTCT AAAATAGATT TTTCTGCCTC AAGACAGAAG ATGGGCGTTC CAGGCAGAGA AGAGCTGCCC 002080 002081 AGTCACGTGC TCTGCTCCAC CTGGTCAGAG ACCCTTGACC TTTAGAAGAC TGGACCTGAG GGCGTGGCTG GTGGACCTGA 002160 002161 GGGCGTGGAT GGTGGACCTG GCCACCCAGC TGTAGCTTTT TGGGTTCCTG TGGTCCCATT TCTTGGGTCA ATCTCACACC 002240 002241 TGGCAGCTCC CAGGAAGACA CCCCCAGGCC CCTCACACTC CTGGGGGCAG CTGGAATTGG CTTCAGGGCG GGACCAGGGG 002320 002321 CCCCATGGGT GTTTGGAATC CCTGATCTGG GTCAGGCACC GGCAGCAGGA TTCCAGCCTG GCCTGGACTC TGGTGTGTCC 002400 002401 CGTTTGAAGA AACCCCGCCC TGTGAAAGTT CAAGTTTAGC ATCCAATGAC CCATTTAAGA GGTTTGCTGA GCCACGTCAC 002480 002481 AGGAGGGTCT GGGTGCAAAC GGAGGTGGCA ACACACAGAG CGAGCCTTGA GCACCCAGGT TACCCCCAGG ACCTCCAGTC 002560 002561 TGGCTTGGGG GCTCCTGCTG TCCTGTGGAG CAGCCCCCTG GGATCAGGGA CGGGGCTGAG CTGGAGAGTG TGCAGGATTG 002640 002641 ATTAATGATG TCTGCCACGG TCAGGCCAAC TGCTGTGTTT CTGGGGCCCA CAAGCTAAAA ATGGTTGGAA AAAAATCAAA 002720 002721 ACATTAATAT TTGTGACATA TGAGAATGCT ATGAAAGTCA ACTTTGCTAT CCATAAATAA AGTTTTATTG ACAT

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