Difference between revisions of "ENST00000447910.2"

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==References==
 
==References==
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[http://www.lncrnadb.org/HAR1B/ Annotation originally sourced from lncRNAdb.]
  
 
{{basic|
 
{{basic|
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sequence = <dnaseq>GTGACCCTGCGGTTAAAACCCGCGCGCTGCAGCATCGCGGAAAACGGGATTCGCCTCATTTGAAACTTGAGGAAAATCTCTAAACACTTTCATTTTGATAGAAACCATTTCCGCCGCTGACGTGCGTCTACGCCCATCATTTCAGCTGACACGTTGCTGTAACGTCTCCTCCGTTTCATGCTCTTTCGAACCCTGTCAGCTGCGGGAAGGAACTTCTAAACTAAAAGCTGGCAAGACTCAGCAGAAAAAAAATATCGAAAGCTGCTTCTGCTGCCCCAGCTTCACTCAGGCCCTGGCTGCTCCTTCACTGGTCTACACTGCTGCCTCCTGGAACCACCCACTCTGCAACCAGGTCTGATGCCCGGTGTGGACATTCAGGGATGAGGTCCCCTGGGGCTAAATGAATGAACAGATTCTGAAAAGCAGAAGCTACGTCCGGGGGTCTCTGGGCCACAAATCACTTTCTGACCTGCAGCCGTGAGGCGTGAGGCTCACTCGGAAGCTCCCGGAACCTGGAGACTGCCCTCACTCAACACTTGAACAAGCAAGGGGCCAGGTTCAATGAAACACCTGCCCGCCCGGCACACCAGGCTCAAAAGCAAGCAAGCAAGCAAACAAACAAACAAAATCAAATCAGGCCTTCACAACTCCCCAAATCATGTGTGAGTTTCTACAGAGCAGAAGCCAAAAATATATGTTATCTAACTAGGTCCTATTTACATATATTTTTATGGCTGCTCTAAAAAATTATCACAAACATAGCGGCTTCACCCCGTTTCCCCTGTTGTGATTATTACACATTGGATGCCTGTATCAAAATATCTCATGGACCCCATAAATAGCAACACCCTGTATGTACTCATGACAATTTTTTAAAAAAGAACACTTACACTTTC</dnaseq>|
 
sequence = <dnaseq>GTGACCCTGCGGTTAAAACCCGCGCGCTGCAGCATCGCGGAAAACGGGATTCGCCTCATTTGAAACTTGAGGAAAATCTCTAAACACTTTCATTTTGATAGAAACCATTTCCGCCGCTGACGTGCGTCTACGCCCATCATTTCAGCTGACACGTTGCTGTAACGTCTCCTCCGTTTCATGCTCTTTCGAACCCTGTCAGCTGCGGGAAGGAACTTCTAAACTAAAAGCTGGCAAGACTCAGCAGAAAAAAAATATCGAAAGCTGCTTCTGCTGCCCCAGCTTCACTCAGGCCCTGGCTGCTCCTTCACTGGTCTACACTGCTGCCTCCTGGAACCACCCACTCTGCAACCAGGTCTGATGCCCGGTGTGGACATTCAGGGATGAGGTCCCCTGGGGCTAAATGAATGAACAGATTCTGAAAAGCAGAAGCTACGTCCGGGGGTCTCTGGGCCACAAATCACTTTCTGACCTGCAGCCGTGAGGCGTGAGGCTCACTCGGAAGCTCCCGGAACCTGGAGACTGCCCTCACTCAACACTTGAACAAGCAAGGGGCCAGGTTCAATGAAACACCTGCCCGCCCGGCACACCAGGCTCAAAAGCAAGCAAGCAAGCAAACAAACAAACAAAATCAAATCAGGCCTTCACAACTCCCCAAATCATGTGTGAGTTTCTACAGAGCAGAAGCCAAAAATATATGTTATCTAACTAGGTCCTATTTACATATATTTTTATGGCTGCTCTAAAAAATTATCACAAACATAGCGGCTTCACCCCGTTTCCCCTGTTGTGATTATTACACATTGGATGCCTGTATCAAAATATCTCATGGACCCCATAAATAGCAACACCCTGTATGTACTCATGACAATTTTTTAAAAAAGAACACTTACACTTTC</dnaseq>|
 
}}
 
}}
[[Category:Intergenic]][[Category:lnc-BHLHE23-2]][[Category:NONHSAG032266]]
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[[Category:Intergenic]][[Category:lnc-BHLHE23-2]][[Category:NONHSAG032266]][[Category:ENSG00000231133.2]][[Category:Transcripts]]

Latest revision as of 02:45, 26 August 2015

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Annotated Information

Name

HAR1B

Characteristics

~900bp in humans. Contains a 'human accelerated region' (HAR). Overlaps with an antisense noncoding RNA, HAR1A (Pollard (2006)). Two splice isoforms, one with 2 exons, one with 3 exons (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

Expression was found in adult brain, ovary and testis in human. Expression level was much lower than HAR1A (Pollard (2006)). Repressed transcriptionally by REST, which causes repression of HAR1B in striatum of Huntington's disease patients (Johnson (2010)). . The mouse locus is expressed during embryonic development (peak at E15) and in adults it is specifically expressed in the brain. Unlike in human, "HAR1B" was expressed at similar levels to "HAR1A" in mouse (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)). Rest of HAR1B sequence has little conservation outside of chimp and macaque (Pollard (2006)). </tab>|

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

Annotation originally sourced from lncRNAdb.

Basic Information

Transcript ID

ENST00000447910.2

Source

Gencode19

Same with

lnc-BHLHE23-2:1,NONHSAT080827

Classification

intergenic

Length

896 nt

Genomic location

chr20-:61726845..61733671

Exon number

2

Exons

61726845..61727535,61733467..61733671

Genome context

Sequence
000001 GTGACCCTGC GGTTAAAACC CGCGCGCTGC AGCATCGCGG AAAACGGGAT TCGCCTCATT TGAAACTTGA GGAAAATCTC 000080
000081 TAAACACTTT CATTTTGATA GAAACCATTT CCGCCGCTGA CGTGCGTCTA CGCCCATCAT TTCAGCTGAC ACGTTGCTGT 000160
000161 AACGTCTCCT CCGTTTCATG CTCTTTCGAA CCCTGTCAGC TGCGGGAAGG AACTTCTAAA CTAAAAGCTG GCAAGACTCA 000240
000241 GCAGAAAAAA AATATCGAAA GCTGCTTCTG CTGCCCCAGC TTCACTCAGG CCCTGGCTGC TCCTTCACTG GTCTACACTG 000320
000321 CTGCCTCCTG GAACCACCCA CTCTGCAACC AGGTCTGATG CCCGGTGTGG ACATTCAGGG ATGAGGTCCC CTGGGGCTAA 000400
000401 ATGAATGAAC AGATTCTGAA AAGCAGAAGC TACGTCCGGG GGTCTCTGGG CCACAAATCA CTTTCTGACC TGCAGCCGTG 000480
000481 AGGCGTGAGG CTCACTCGGA AGCTCCCGGA ACCTGGAGAC TGCCCTCACT CAACACTTGA ACAAGCAAGG GGCCAGGTTC 000560
000561 AATGAAACAC CTGCCCGCCC GGCACACCAG GCTCAAAAGC AAGCAAGCAA GCAAACAAAC AAACAAAATC AAATCAGGCC 000640
000641 TTCACAACTC CCCAAATCAT GTGTGAGTTT CTACAGAGCA GAAGCCAAAA ATATATGTTA TCTAACTAGG TCCTATTTAC 000720
000721 ATATATTTTT ATGGCTGCTC TAAAAAATTA TCACAAACAT AGCGGCTTCA CCCCGTTTCC CCTGTTGTGA TTATTACACA 000800
000801 TTGGATGCCT GTATCAAAAT ATCTCATGGA CCCCATAAAT AGCAACACCC TGTATGTACT CATGACAATT TTTTAAAAAA 000880
000881 GAACACTTAC ACTTTC
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