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HOTAIR HOX transcript antisense RNA [ Homo sapiens (human) ]

Gene ID: 100124700, updated on 15-Jul-2018
Official Symbol
HOTAIRprovided by HGNC
Official Full Name
HOX transcript antisense RNAprovided by HGNC
Primary source
See related
Ensembl:ENSG00000228630 MIM:611400
Gene type
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
This gene is located within the Homeobox C (HOXC) gene cluster on chromosome 12 and is co-expressed with the HOXC genes. It functions through an RNA product, which binds lysine specific demethylase 1 (LSD1) and Polycomb repressive complex 2 (PRC2), and servers as a scaffold to assemble these regulators at the HOXD gene cluster, thereby promoting epigenetic repression of HOXD. This gene is highly expressed in multiple tumors. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2017]
Biased expression in testis (RPKM 1.6), skin (RPKM 1.2) and 6 other tissues See more
See HOTAIR in Genome Data Viewer
Exon count:
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (53962308..53974956, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54356092..54368740, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene HOXC13 antisense RNA Neighboring gene homeobox C13 Neighboring gene uncharacterized LOC105369775 Neighboring gene homeobox C12 Neighboring gene NUP98-HOXC11 recombination region Neighboring gene homeobox C11 Neighboring gene HOXC11-HOXC10 intergenic CAGE-defined high expression enhancer Neighboring gene HOXC cluster antisense RNA 3 Neighboring gene homeobox C10

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Products Interactant Other Gene Complex Source Pubs Description


Other Names

  • HOX transcript antisense RNA (non-protein coding)
  • HOXC cluster antisense RNA 4 (non-protein coding)
  • hox transcript antisense intergenic RNA

Clone Names

  • FLJ41747

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IEA
Inferred from Electronic Annotation
more info
Process Evidence Code Pubs
chromatin silencing IEA
Inferred from Electronic Annotation
more info

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.


  1. NR_003716.3 RNA Sequence

    Status: REVIEWED

    Transcript Variant: This variant (2) has an additional exon in the 3' region, compared to variant 1. Its 5' end has not been determined.
    Source sequence(s)
    AA399272, AC012531, AK123741, DA905601
  2. NR_047517.1 RNA Sequence

    Status: REVIEWED

    Transcript Variant: This variant (1) consists of six exons.
    Source sequence(s)
    AA399272, AC012531, DA905601
  3. NR_047518.1 RNA Sequence

    Status: REVIEWED

    Transcript Variant: This variant (3) has an alternate 5' sequence and lacks an internal exon in the 5' region, compared to variant 1.
    Source sequence(s)
    AC012531, DA907429

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly


  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    53962308..53974956 complement
    GenBank, FASTA, Sequence Viewer (Graphics)
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