ENST00000554403.1

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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 A