U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 100124700, updated on 16-Apr-2024

Summary

Go to the top of the page Help
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
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. The lncRNA HOTAIR: a pleiotropic regulator of epithelial cell plasticity. Amicone L, et al. J Exp Clin Cancer Res, 2023 Jun 13. PMID 37308974, Free PMC Article
  2. LncRNA HOTAIR as a ceRNA is related to breast cancer risk and prognosis. Qian L, et al. Breast Cancer Res Treat, 2023 Aug. PMID 37294527
  3. HOTAIR: a potential metastatic, drug-resistant and prognostic regulator of breast cancer. Raju GSR, et al. Mol Cancer, 2023 Mar 30. PMID 36997931, Free PMC Article
  4. Genetic Variants of HOTAIR Associated with Colorectal Cancer: A Case-Control Study in the Saudi Population. Alzeer HS, et al. Genes (Basel), 2023 Feb 26. PMID 36980864, Free PMC Article
  5. HOTAIR knockdown impairs metastasis of cervical cancer cells by down-regulating metastasis-related genes. Shi L, et al. J Obstet Gynaecol, 2023 Dec. PMID 36972141

See all (491) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The association of FSCN1 (rs852479, rs1640233) and HOTAIR (rs920778) polymorphisms with the risk of breast cancer in Egyptian women.
    Title: The association of FSCN1 (rs852479, rs1640233) and HOTAIR (rs920778) polymorphisms with the risk of breast cancer in Egyptian women.
  2. Adolescent polycystic ovary syndrome without obesity: HOTAIR rs1443512 genotype relates to fat mass and to the redistribution of fat mass on low-dose pioglitazone.
    Title: Adolescent polycystic ovary syndrome without obesity: HOTAIR rs1443512 genotype relates to fat mass and to the redistribution of fat mass on low-dose pioglitazone.
  3. Roles of HOTAIR Long Non-coding RNA in Gliomas and Other CNS Disorders.
    Title: Roles of HOTAIR Long Non-coding RNA in Gliomas and Other CNS Disorders.
  4. Potential role of the lncRNA "HOTAIR"/miRNA "206"/BDNF network in the alteration in expression of synaptic plasticity gene arc and BDNF level in sera of patients with heroin use disorder through the PI3K/AKT/mTOR pathway compared to the controls.
    Title: Potential role of the lncRNA "HOTAIR"/miRNA "206"/BDNF network in the alteration in expression of synaptic plasticity gene arc and BDNF level in sera of patients with heroin use disorder through the PI3K/AKT/mTOR pathway compared to the controls.
  5. LncRNA HOTAIR Inhibits miR-19a-3p to Alleviate Foam Cell Formation and Inflammatory Response in Atherosclerosis.
    Title: LncRNA HOTAIR Inhibits miR-19a-3p to Alleviate Foam Cell Formation and Inflammatory Response in Atherosclerosis.
  6. HOTAIR: A key regulator of the Wnt/beta-catenin signaling cascade in cancer progression and treatment.
    Title: HOTAIR: A key regulator of the Wnt/β-catenin signaling cascade in cancer progression and treatment.
  7. LncRNA HOTTIP as a diagnostic biomarker for acute respiratory distress syndrome in patients with sepsis and to predict the short-term clinical outcome: a case-control study.
    Title: LncRNA HOTTIP as a diagnostic biomarker for acute respiratory distress syndrome in patients with sepsis and to predict the short-term clinical outcome: a case-control study.
  8. Circulating ESR1, long non-coding RNA HOTAIR and microRNA-130a gene expression as biomarkers for breast cancer stage and metastasis.
    Title: Circulating ESR1, long non-coding RNA HOTAIR and microRNA-130a gene expression as biomarkers for breast cancer stage and metastasis.
  9. The long non-coding RNA HOTAIR contributes to joint-specific gene expression in rheumatoid arthritis.
    Title: The long non-coding RNA HOTAIR contributes to joint-specific gene expression in rheumatoid arthritis.
  10. Association of lncRNA THRIL, HOTAIR genes variations and expression levels with pulmonary tuberculosis.
    Title: Association of lncRNA THRIL, HOTAIR genes variations and expression levels with pulmonary tuberculosis.
Submit: New GeneRIF Correction See all GeneRIFs (481)

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Homology

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)

Go to the top of the page Help

NEW Try the new Transcript table

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)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Miscellaneous