Difference between revisions of "ENST00000554403.1"

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sequence = <dnaseq>GCATTGCTGTGTGTCTGCCACCGCTGCCTGGCACTCATGGGGCCGTGTGTGTGTGTATGTGTGTGTGCGCGCATGTACATGTACGCATAAGCGTGTGCTGTATGTGAGCCTCCTGGGCATGGGTGGGGGTTGGCATTGCGGTTGCCAATCTAGTGTACAACCAGAAGGACAGAGGGATGGAGTGGAAGAAGGAGGGGAGAGGCTTGGGGTCTGGGAGGGGAGAAGAGGGTGCATGAGTTGCTTCATGCTGCCTGCTTACAGGCATTGGCATTGTAGCTGCCACCCTTGTGCCCACGGAGATGGGAGGAGGCGAGTGGAGGGCGCAGCGGCAGGAGTCCTGTGCTCTGGGAGGAAGGCTTTGTACATGGGAGCTGTTGGCATCACATCTGTCAGGCCGGTGCCCAGAACTGGGGCAATGGAGACTGGGGGATCCAGGAAGCAGGGAGGAGGGGCAGAATGTGTTTCTGATGTTGCTGTCCCTCTAGAAGCTCAGCTCTGAAAAATGGTTGGAGTATGAGGTGATTAGTGCTCTTCCAGCTTGAGGAAGTAAAGTGGTGGAGAGAGTAGCCAGGGAAGTGCCAAGAAACAGTCTACGAGCCAGGGAGGAGGGAGTGTGCCACCGTACCCAGGGAGAACTTGTTGGGGCTGGCAATCTGGCCCTTTGTCAGAGTATTGAAGGAGACAGCAAGAGGACCAGATGTGAGGTGGGTGGGTGCTGGCACTGCCCATGGCACCTGGCACAGGCTCTGGCATTGTGTGGAACAGGGGAGGTTGACAGTGCCTCTTGCCAATCTGGTTGAGAGGGCTATTGTGCCAGGAGTGAGAAGGAAGGAGGTGAAACATTTCGGGAGGTGGGGTGTTTGGGAGACCAGATTTTTTTCTGCCAGGTCCTCCTTCCCCTTCCCTCTTAGGCATGGGGAGTGGAGCAACAGACGGAGAGTGGCATGAAGACACAAAGGAGGAAGCACACCATTGCCAAGACCCCAAGGAAGAAGGATGGAAAGCGCTGGCAGTCCTGCCTGGCCCCCAGCCAGTTCCCTGCTGAAGATGGCCAGATCCCCTTGTCTGGCCTCCCAGCTCTGGCACCAGATTGGGATGGTGGCCTGTCCCCAGTGAGAAGGAGGTGGCAAGGAGGCTGTCTCTTGCACTTTGCAAGATGCTTAAGTAGAGACAGGGTTTCACCATGTTGTCCAGGATGGTCTCTATCTCCTGACTACCTGACCCGCCCACCTTGGCCTGGGATTACAGGCGTGAGCCACTGCGCCCGGCTGGAAGGAAAACATTCTGAGTGACCGTGTATGTAAATAAGTCTTTCTGGTTATTTTATTCTGTGAACCTGTGTGATGTAATGACTGCATTTAAATAGTATTACAACAAAAACTAATTGTAATAATAGTAAATAGCTAACATCTTTAAATGTTTGCCATGGGCCAGGCACCGTGCTAGGCCCTCGGCAAGTATCACATCACCTAATCCTCCACTTCAATCTGATGCAATAGATGTAGCTATTCATTCCTATTTTACAAACATGGAGACTGATTTAGATGGGTTAAGTAATTTTTAAGATCTCCTGCTTAAAAAGAAGTAGAGTTGAGATTGGAACTCAGGTAGCCTGATGTCAGTACCTCTGCTCTTGGGTTAATTTGTAAGCTTCTGAACTCTGGCTGGTATGCATTTTGAATGAGGTCTTTTGAGTCTGATTGTATTACTCTGTGTGTCACCTTGAGCATATGTGCTATCATGTTCCGCCTGAAGGTGCTAGATGGCTGTCTTCCATTTGGTTTGTTTCTTAGTATAAGATGGACCAGAAGAGGAGCACTGCTTTGCGCAACTCCAGGGTGCGTCATTCACACTGCAGTCCATGCAGGGGCACTGGCCATGCCCTGTGTGAAGGAAGGGAAGGAGCGGGAGGGAGGGAGTGGGAACAGGAGGGAAGGGATAGATAATGGCGGGTAGTGTTCTTTGAATGATATGTGTACCCATTTGTGACAACATCTCTTAAAGTTGAAGGTCTACACATGTGTATCCATATTAGCATATGAACTTCATCAGACAAGCACTCTCCCTCCAACAGAGGGAGACCCTGTCTCAAAAAACAAAAAAAAATAGCCTTTAGAGTCAGACAGACCTGGAATCAAATTCTAGTTCTGTTTCTTAATATGTAAATGACCTCAGGTAAGTTGCGTAAAGTCTCAATTTAGTCTCTTCATATAGAGAATGGGGCAGGCCGGGCACGCGCCTATAATTCCAGCACTTTGGGAGGCCGAGGTGGGTGGATCATTGGAGGTCAGGAGCTTGAGACCAGCCTGGCCAACACGGTGAAACCCTGTCTCTACTAAAAATACAAAAAAAATGAGCCGGGCGTGGTGGCATGCACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGAAGAATCGCTTGAACCCGGGAAGCAGAGGTTGTAGTGAGCCGAGATTGCACCACTGCACTCCAGCCTGGGTGACAGAGTGAGACCCTGTCTAAAAACAAACACATCAGAAACAG</dnaseq>|
 
sequence = <dnaseq>GCATTGCTGTGTGTCTGCCACCGCTGCCTGGCACTCATGGGGCCGTGTGTGTGTGTATGTGTGTGTGCGCGCATGTACATGTACGCATAAGCGTGTGCTGTATGTGAGCCTCCTGGGCATGGGTGGGGGTTGGCATTGCGGTTGCCAATCTAGTGTACAACCAGAAGGACAGAGGGATGGAGTGGAAGAAGGAGGGGAGAGGCTTGGGGTCTGGGAGGGGAGAAGAGGGTGCATGAGTTGCTTCATGCTGCCTGCTTACAGGCATTGGCATTGTAGCTGCCACCCTTGTGCCCACGGAGATGGGAGGAGGCGAGTGGAGGGCGCAGCGGCAGGAGTCCTGTGCTCTGGGAGGAAGGCTTTGTACATGGGAGCTGTTGGCATCACATCTGTCAGGCCGGTGCCCAGAACTGGGGCAATGGAGACTGGGGGATCCAGGAAGCAGGGAGGAGGGGCAGAATGTGTTTCTGATGTTGCTGTCCCTCTAGAAGCTCAGCTCTGAAAAATGGTTGGAGTATGAGGTGATTAGTGCTCTTCCAGCTTGAGGAAGTAAAGTGGTGGAGAGAGTAGCCAGGGAAGTGCCAAGAAACAGTCTACGAGCCAGGGAGGAGGGAGTGTGCCACCGTACCCAGGGAGAACTTGTTGGGGCTGGCAATCTGGCCCTTTGTCAGAGTATTGAAGGAGACAGCAAGAGGACCAGATGTGAGGTGGGTGGGTGCTGGCACTGCCCATGGCACCTGGCACAGGCTCTGGCATTGTGTGGAACAGGGGAGGTTGACAGTGCCTCTTGCCAATCTGGTTGAGAGGGCTATTGTGCCAGGAGTGAGAAGGAAGGAGGTGAAACATTTCGGGAGGTGGGGTGTTTGGGAGACCAGATTTTTTTCTGCCAGGTCCTCCTTCCCCTTCCCTCTTAGGCATGGGGAGTGGAGCAACAGACGGAGAGTGGCATGAAGACACAAAGGAGGAAGCACACCATTGCCAAGACCCCAAGGAAGAAGGATGGAAAGCGCTGGCAGTCCTGCCTGGCCCCCAGCCAGTTCCCTGCTGAAGATGGCCAGATCCCCTTGTCTGGCCTCCCAGCTCTGGCACCAGATTGGGATGGTGGCCTGTCCCCAGTGAGAAGGAGGTGGCAAGGAGGCTGTCTCTTGCACTTTGCAAGATGCTTAAGTAGAGACAGGGTTTCACCATGTTGTCCAGGATGGTCTCTATCTCCTGACTACCTGACCCGCCCACCTTGGCCTGGGATTACAGGCGTGAGCCACTGCGCCCGGCTGGAAGGAAAACATTCTGAGTGACCGTGTATGTAAATAAGTCTTTCTGGTTATTTTATTCTGTGAACCTGTGTGATGTAATGACTGCATTTAAATAGTATTACAACAAAAACTAATTGTAATAATAGTAAATAGCTAACATCTTTAAATGTTTGCCATGGGCCAGGCACCGTGCTAGGCCCTCGGCAAGTATCACATCACCTAATCCTCCACTTCAATCTGATGCAATAGATGTAGCTATTCATTCCTATTTTACAAACATGGAGACTGATTTAGATGGGTTAAGTAATTTTTAAGATCTCCTGCTTAAAAAGAAGTAGAGTTGAGATTGGAACTCAGGTAGCCTGATGTCAGTACCTCTGCTCTTGGGTTAATTTGTAAGCTTCTGAACTCTGGCTGGTATGCATTTTGAATGAGGTCTTTTGAGTCTGATTGTATTACTCTGTGTGTCACCTTGAGCATATGTGCTATCATGTTCCGCCTGAAGGTGCTAGATGGCTGTCTTCCATTTGGTTTGTTTCTTAGTATAAGATGGACCAGAAGAGGAGCACTGCTTTGCGCAACTCCAGGGTGCGTCATTCACACTGCAGTCCATGCAGGGGCACTGGCCATGCCCTGTGTGAAGGAAGGGAAGGAGCGGGAGGGAGGGAGTGGGAACAGGAGGGAAGGGATAGATAATGGCGGGTAGTGTTCTTTGAATGATATGTGTACCCATTTGTGACAACATCTCTTAAAGTTGAAGGTCTACACATGTGTATCCATATTAGCATATGAACTTCATCAGACAAGCACTCTCCCTCCAACAGAGGGAGACCCTGTCTCAAAAAACAAAAAAAAATAGCCTTTAGAGTCAGACAGACCTGGAATCAAATTCTAGTTCTGTTTCTTAATATGTAAATGACCTCAGGTAAGTTGCGTAAAGTCTCAATTTAGTCTCTTCATATAGAGAATGGGGCAGGCCGGGCACGCGCCTATAATTCCAGCACTTTGGGAGGCCGAGGTGGGTGGATCATTGGAGGTCAGGAGCTTGAGACCAGCCTGGCCAACACGGTGAAACCCTGTCTCTACTAAAAATACAAAAAAAATGAGCCGGGCGTGGTGGCATGCACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGAAGAATCGCTTGAACCCGGGAAGCAGAGGTTGTAGTGAGCCGAGATTGCACCACTGCACTCCAGCCTGGGTGACAGAGTGAGACCCTGTCTAAAAACAAACACATCAGAAACAG</dnaseq>|
 
}}
 
}}
[[Category:Intergenic]][[Category:lnc-THTPA-2]][[Category:NONHSAG014500]][[Category:ENSG00000157306.10]]
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[[Category:Intergenic]][[Category:lnc-THTPA-2]][[Category:NONHSAG014500]][[Category:ENSG00000157306.10]][[Category:Transcripts]]

Revision as of 11:16, 16 October 2014

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Annotated Information

Name

Zfhx2as: zinc finger homeobox 2, antisense

Characteristics

Antisense transcription begins 6-10kb downstream of the Zfhx2 polyA site and ends in first exon of Zfhx2. Alternatively spliced. Multiple start sites. Estimated as up to ~30 kb in length.

Function

Zfhx2as negatively regulates the expression of Zfhx2. Knockout of antisense RNA lead to up-regulation of Zfhx2 expression, with coding gene expression in areas previously showing only expression of the antisense transcript. The same effect was seen in a mutant where Zfhx2 and Zfhx2as no longer overlapped strongly suggesting Zfhx2as negatively regulates Zfhx2.

Expression

Expressed in a number of specific regions in the developing mouse brain including the rostral migratory stream (RMS). Antisense RNA was expressed in a complementary manner to the sense coding sequence. For example the antisense RNA was expressed initially in hippocampal development, with the sense RNA only starting to be expressed when antisense transcription declined. Or, alternatively in the dorsal forebrain where sense and antisense transcripts are expressed in different layers of cells at the same stage. Expression was highest in mid-gestation E13.5-E16.5. Adult expression specific to brain, with expression in areas of adult neurogenesis.

Conservation

Identified in rodents and humans.

Misc

NCBI Gene and Refseq sequence given for Zfhx2as (provided here) is only a partial sequence from the center of the antisense transcript. Since full length transcript not defined, UCSC browser links are best estimates of transcripts. Mouse transcript comes from a Scripture transcript defined by Guttman (2010).

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

ENST00000554403.1

Source

Gencode19

Same with

lnc-THTPA-2:5,NONHSAT035910

Classification

intergenic

Length

2524 nt

Genomic location

chr14+:23982558..24013485

Exon number

3

Exons

23982558..23983625,24011368..24011464,24012127..24013485

Genome context

Sequence
000001 GCATTGCTGT GTGTCTGCCA CCGCTGCCTG GCACTCATGG GGCCGTGTGT GTGTGTATGT GTGTGTGCGC GCATGTACAT 000080
000081 GTACGCATAA GCGTGTGCTG TATGTGAGCC TCCTGGGCAT GGGTGGGGGT TGGCATTGCG GTTGCCAATC TAGTGTACAA 000160
000161 CCAGAAGGAC AGAGGGATGG AGTGGAAGAA GGAGGGGAGA GGCTTGGGGT CTGGGAGGGG AGAAGAGGGT GCATGAGTTG 000240
000241 CTTCATGCTG CCTGCTTACA GGCATTGGCA TTGTAGCTGC CACCCTTGTG CCCACGGAGA TGGGAGGAGG CGAGTGGAGG 000320
000321 GCGCAGCGGC AGGAGTCCTG TGCTCTGGGA GGAAGGCTTT GTACATGGGA GCTGTTGGCA TCACATCTGT CAGGCCGGTG 000400
000401 CCCAGAACTG GGGCAATGGA GACTGGGGGA TCCAGGAAGC AGGGAGGAGG GGCAGAATGT GTTTCTGATG TTGCTGTCCC 000480
000481 TCTAGAAGCT CAGCTCTGAA AAATGGTTGG AGTATGAGGT GATTAGTGCT CTTCCAGCTT GAGGAAGTAA AGTGGTGGAG 000560
000561 AGAGTAGCCA GGGAAGTGCC AAGAAACAGT CTACGAGCCA GGGAGGAGGG AGTGTGCCAC CGTACCCAGG GAGAACTTGT 000640
000641 TGGGGCTGGC AATCTGGCCC TTTGTCAGAG TATTGAAGGA GACAGCAAGA GGACCAGATG TGAGGTGGGT GGGTGCTGGC 000720
000721 ACTGCCCATG GCACCTGGCA CAGGCTCTGG CATTGTGTGG AACAGGGGAG GTTGACAGTG CCTCTTGCCA ATCTGGTTGA 000800
000801 GAGGGCTATT GTGCCAGGAG TGAGAAGGAA GGAGGTGAAA CATTTCGGGA GGTGGGGTGT TTGGGAGACC AGATTTTTTT 000880
000881 CTGCCAGGTC CTCCTTCCCC TTCCCTCTTA GGCATGGGGA GTGGAGCAAC AGACGGAGAG TGGCATGAAG ACACAAAGGA 000960
000961 GGAAGCACAC CATTGCCAAG ACCCCAAGGA AGAAGGATGG AAAGCGCTGG CAGTCCTGCC TGGCCCCCAG CCAGTTCCCT 001040
001041 GCTGAAGATG GCCAGATCCC CTTGTCTGGC CTCCCAGCTC TGGCACCAGA TTGGGATGGT GGCCTGTCCC CAGTGAGAAG 001120
001121 GAGGTGGCAA GGAGGCTGTC TCTTGCACTT TGCAAGATGC TTAAGTAGAG ACAGGGTTTC ACCATGTTGT CCAGGATGGT 001200
001201 CTCTATCTCC TGACTACCTG ACCCGCCCAC CTTGGCCTGG GATTACAGGC GTGAGCCACT GCGCCCGGCT GGAAGGAAAA 001280
001281 CATTCTGAGT GACCGTGTAT GTAAATAAGT CTTTCTGGTT ATTTTATTCT GTGAACCTGT GTGATGTAAT GACTGCATTT 001360
001361 AAATAGTATT ACAACAAAAA CTAATTGTAA TAATAGTAAA TAGCTAACAT CTTTAAATGT TTGCCATGGG CCAGGCACCG 001440
001441 TGCTAGGCCC TCGGCAAGTA TCACATCACC TAATCCTCCA CTTCAATCTG ATGCAATAGA TGTAGCTATT CATTCCTATT 001520
001521 TTACAAACAT GGAGACTGAT TTAGATGGGT TAAGTAATTT TTAAGATCTC CTGCTTAAAA AGAAGTAGAG TTGAGATTGG 001600
001601 AACTCAGGTA GCCTGATGTC AGTACCTCTG CTCTTGGGTT AATTTGTAAG CTTCTGAACT CTGGCTGGTA TGCATTTTGA 001680
001681 ATGAGGTCTT TTGAGTCTGA TTGTATTACT CTGTGTGTCA CCTTGAGCAT ATGTGCTATC ATGTTCCGCC TGAAGGTGCT 001760
001761 AGATGGCTGT CTTCCATTTG GTTTGTTTCT TAGTATAAGA TGGACCAGAA GAGGAGCACT GCTTTGCGCA ACTCCAGGGT 001840
001841 GCGTCATTCA CACTGCAGTC CATGCAGGGG CACTGGCCAT GCCCTGTGTG AAGGAAGGGA AGGAGCGGGA GGGAGGGAGT 001920
001921 GGGAACAGGA GGGAAGGGAT AGATAATGGC GGGTAGTGTT CTTTGAATGA TATGTGTACC CATTTGTGAC AACATCTCTT 002000
002001 AAAGTTGAAG GTCTACACAT GTGTATCCAT ATTAGCATAT GAACTTCATC AGACAAGCAC TCTCCCTCCA ACAGAGGGAG 002080
002081 ACCCTGTCTC AAAAAACAAA AAAAAATAGC CTTTAGAGTC AGACAGACCT GGAATCAAAT TCTAGTTCTG TTTCTTAATA 002160
002161 TGTAAATGAC CTCAGGTAAG TTGCGTAAAG TCTCAATTTA GTCTCTTCAT ATAGAGAATG GGGCAGGCCG GGCACGCGCC 002240
002241 TATAATTCCA GCACTTTGGG AGGCCGAGGT GGGTGGATCA TTGGAGGTCA GGAGCTTGAG ACCAGCCTGG CCAACACGGT 002320
002321 GAAACCCTGT CTCTACTAAA AATACAAAAA AAATGAGCCG GGCGTGGTGG CATGCACCTG TAATCCCAGC TACTCAGGAG 002400
002401 GCTGAGGCAG AAGAATCGCT TGAACCCGGG AAGCAGAGGT TGTAGTGAGC CGAGATTGCA CCACTGCACT CCAGCCTGGG 002480
002481 TGACAGAGTG AGACCCTGTC TAAAAACAAA CACATCAGAA ACAG
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