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

Gene ID: 100124700, updated on 19-Feb-2024

Summary

Official Symbol
HOTAIRprovided by HGNC
Official Full Name
HOX transcript antisense RNAprovided by HGNC
Primary source
HGNC:HGNC:33510
See related
Ensembl:ENSG00000228630 MIM:611400; AllianceGenome:HGNC:33510
Gene type
ncRNA
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072
Summary
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 serves 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, Feb 2019]
Expression
Biased expression in testis (RPKM 1.6), skin (RPKM 1.2) and 6 other tissues See more
Orthologs
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Genomic context

See HOTAIR in Genome Data Viewer
Location:
12q13.13
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (53962312..53974954, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53927801..53940446, complement)
105.20220307 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 H3K4me1 hESC enhancer GRCh37_chr12:54345326-54345913 Neighboring gene uncharacterized LOC105369775 Neighboring gene homeobox C12 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:54355207-54355431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54360165-54361069 Neighboring gene NUP98-HOXC11 recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54368136-54368730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6430 Neighboring gene homeobox C11 Neighboring gene HOXC11-HOXC10 intergenic CAGE-defined high expression enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54379714-54380594 Neighboring gene HOXC cluster antisense RNA 3 Neighboring gene homeobox C10 Neighboring gene microRNA 196a-2

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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

NCBI Reference Sequences (RefSeq)

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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.

RNA

  1. NR_003716.4 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  2. NR_047517.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  3. NR_047518.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  4. NR_186237.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  5. NR_186238.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  6. NR_186239.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  7. NR_186240.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  8. NR_186241.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
    Related
    ENST00000424518.5
  9. NR_186242.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  10. NR_186243.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  11. NR_186244.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  12. NR_186245.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  13. NR_186246.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  14. NR_186247.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  15. NR_186248.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  16. NR_186249.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
  17. NR_186250.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    53962312..53974954 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53927801..53940446 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)