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

Gene ID: 100124700, updated on 2-Nov-2024

Summary

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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

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See HOTAIR in Genome Data Viewer
Location:
12q13.13
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (53962312..53974954, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53927801..53940446, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54356096..54368738, 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. Long non-coding RNA HOTAIR promotes tumorigenesis and forecasts a poor prognosis in cholangiocarcinoma. Qin W, et al. Sci Rep, 2018 Aug 15. PMID 30111807, Free PMC Article
  2. Long noncoding RNA HOTAIR can serve as a common molecular marker for lymph node metastasis: a meta-analysis. Cai B, et al. Tumour Biol, 2014 Sep. PMID 25017366
  3. Long non-coding RNA HOTAIR promotes osteoarthritis progression via miR-17-5p/FUT2/β-catenin axis. Hu J, et al. Cell Death Dis, 2018 Jun 15. PMID 29907764, Free PMC Article
  4. Rs4759314 polymorphism located in HOTAIR is associated with the risk of congenital heart disease by alternating downstream signaling via reducing its expression. Li Y, et al. J Cell Biochem, 2018 Nov. PMID 29932240
  5. The prognostic value of HOTAIR for predicting long-term prognosis of patients with gastrointestinal cancers. Zhang Y, et al. Medicine (Baltimore), 2018 Jun. PMID 29952959, Free PMC Article

See all (504) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LncRNA HOTAIR promotes the migration and invasion of cervical cancer through DNMT3B/LATS1/ YAP1 pS127 axis.
    Title: LncRNA HOTAIR promotes the migration and invasion of cervical cancer through DNMT3B/LATS1/ YAP1 pS127 axis.
  2. A Study on Associations of Long Noncoding RNA HOTAIR Polymorphisms With Genetic Susceptibility to Chronic Kidney Disease.
    Title: A Study on Associations of Long Noncoding RNA HOTAIR Polymorphisms With Genetic Susceptibility to Chronic Kidney Disease.
  3. Long non-coding RNA HOTAIR: from pan-cancer analysis to colorectal cancer-related uridine metabolism.
    Title: Long non-coding RNA HOTAIR: from pan-cancer analysis to colorectal cancer-related uridine metabolism.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (480)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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)

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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
    Related
    ENST00000717836.1

  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
    ENST00000424518.6

  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
    Related
    ENST00000717832.1

  17. NR_186250.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC012531
    Related
    ENST00000717834.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

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Chemical Information
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