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. Th... See more...

Aliases for HOTAIR Gene

Data sources for HOTAIR Gene:

RNA type for HOTAIR Gene

lncRNA

Aliases for HOTAIR Gene

External Ids for HOTAIR Gene

Previous GeneCards Identifiers for HOTAIR Gene

  • GC00U922319
  • GC12U900912
  • GC12M052644
  • GC12M054356
  • GC12M051393

Summaries for HOTAIR Gene

Entrez Gene Summary for HOTAIR Gene

  • 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]

GeneCards Summary for HOTAIR Gene

HOTAIR (HOX Transcript Antisense RNA) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with HOTAIR include Gastric Adenocarcinoma and Pre-Eclampsia. Among its related pathways are LncRNA-mediated mechanisms of therapeutic resistance.

Gene Wiki entry for HOTAIR Gene

Rfam classification for HOTAIR Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary and piRNA Summary for HOTAIR Gene

Genomics for HOTAIR Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HOTAIR Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOTAIR on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the HOTAIR gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • FOXO1a

Genomic Locations for HOTAIR Gene

Latest Assembly
chr12:53,962,307-53,974,957
(GRCh38/hg38)
Size:
12,651 bases
Orientation:
Minus strand

Previous Assembly
chr12:54,356,092-54,368,740
(GRCh37/hg19 by Entrez Gene)
Size:
12,649 bases
Orientation:
Minus strand

chr12:54,356,092-54,368,740
(GRCh37/hg19 by Ensembl)
Size:
12,649 bases
Orientation:
Minus strand

Genomic View for HOTAIR Gene

Genes around HOTAIR on UCSC Golden Path with GeneCards custom track
HOTAIR in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
HOTAIR Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOTAIR Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOTAIR Gene

Proteins for HOTAIR Gene

Post-translational modifications for HOTAIR Gene

No Post-translational modifications

No data available for DME Specific Peptides for HOTAIR Gene

Domains & Families for HOTAIR Gene

Gene Families for HOTAIR Gene

genes like me logo Genes that share domains with HOTAIR: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for HOTAIR Gene

Function for HOTAIR Gene

Phenotypes From GWAS Catalog for HOTAIR Gene

Gene Ontology (GO) - Molecular Function for HOTAIR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with HOTAIR: view

Phenotypes for HOTAIR Gene

genes like me logo Genes that share phenotypes with HOTAIR: view

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HOTAIR Gene

Localization for HOTAIR Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HOTAIR gene
Compartment Confidence
nucleus 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
cytosol 2
endoplasmic reticulum 1
endosome 1
lysosome 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for HOTAIR Gene

Pathways & Interactions for HOTAIR Gene

genes like me logo Genes that share pathways with HOTAIR: view

Pathways by source for HOTAIR Gene

1 BioSystems pathway for HOTAIR Gene

Gene Ontology (GO) - Biological Process for HOTAIR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006342 chromatin silencing IEA --
genes like me logo Genes that share ontologies with HOTAIR: view

No data available for Interacting Proteins and SIGNOR curated interactions for HOTAIR Gene

Drugs & Compounds for HOTAIR Gene

(1) Drugs for HOTAIR Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Platinum compounds Pharma 0
genes like me logo Genes that share compounds with HOTAIR: view

Transcripts for HOTAIR Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for HOTAIR Gene

RNAcentral Transcript ID RNA Type Length (nts) # of Sources Source Identifiers and Annotations
URS0000301B08_9606 lncRNA 2428 3

Ensembl: ENST00000424518 (view in UCSC) ,

LNCipedia: HOTAIR:1,

NONCODE: NONHSAT028510.2,

URS000075EF05_9606 lncRNA 2341 3

RefSeq: NR_047518,

LNCipedia: HOTAIR:5,

NONCODE: NONHSAT028509.2,

URS00001A335C_9606 lncRNA 918 3

Ensembl: ENST00000455246 (view in UCSC) ,

LncBook: HSALNT0189447,

LNCipedia: HOTAIR:3,

URS000019A694_9606 lncRNA 572 3

Ensembl: ENST00000425595 (view in UCSC) ,

LNCipedia: HOTAIR:10,

NONCODE: NONHSAT028513.2,

URS000011D1F0_9606 lncRNA 567 3

Ensembl: ENST00000453875 (view in UCSC) ,

LNCipedia: HOTAIR:9,

NONCODE: NONHSAT028514.2,

HOTAIR in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for HOTAIR Gene

9 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for HOTAIR Gene

No ASD Table

Relevant External Links for HOTAIR Gene

GeneLoc Exon Structure for
HOTAIR

Expression for HOTAIR Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HOTAIR Gene

mRNA differential expression in normal tissues according to GTEx for HOTAIR Gene

This gene is overexpressed in Artery - Tibial (x18.3), Skin - Sun Exposed (Lower leg) (x6.6), and Testis (x4.7).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HOTAIR

SOURCE GeneReport for Unigene cluster for HOTAIR Gene:

Hs.197076

Evidence on tissue expression from TISSUES for HOTAIR Gene

  • Lymph node(2.1)
  • Skin(2)
  • Blood(2)
  • Intestine(2)
  • Liver(2)
genes like me logo Genes that share expression patterns with HOTAIR: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOTAIR Gene

Orthologs for HOTAIR Gene

Evolution for HOTAIR Gene

ENSEMBL:
Gene Tree for HOTAIR (if available)
TreeFam:
Gene Tree for HOTAIR (if available)
Alliance of Genome Resources:
Additional Orthologs for HOTAIR

No data available for Orthologs for HOTAIR Gene

Paralogs for HOTAIR Gene

No data available for Paralogs for HOTAIR Gene

Variants for HOTAIR Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HOTAIR Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for HOTAIR Gene

Variant ID Type Subtype PubMed ID
esv2759900 CNV gain+loss 17122850
nsv428282 CNV gain 18775914
nsv826379 CNV gain 20364138

Additional Variant Information for HOTAIR Gene

Human Gene Mutation Database (HGMD)
HOTAIR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOTAIR
Leiden Open Variation Database (LOVD)
HOTAIR

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for HOTAIR Gene

Disorders for HOTAIR Gene

MalaCards: The human disease database

(71) MalaCards diseases for HOTAIR Gene - From: LNC, COP, and GCD

Disorder Aliases PubMed IDs
gastric adenocarcinoma
  • adenocarcinoma of stomach
pre-eclampsia
  • gestational hypertension
gastrointestinal system cancer
  • digestive system cancer
cerebrovascular disease
  • cerebrovascular accident
triple-receptor negative breast cancer
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HOTAIR

genes like me logo Genes that share disorders with HOTAIR: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HOTAIR Gene

Publications for HOTAIR Gene

  1. Serum HOTAIR and GAS5 levels as predictors of survival in patients with glioblastoma. (PMID: 28926136) Shen J … Zhao H (Molecular carcinogenesis 2018) 3 72
  2. Long Noncoding RNA HOTAIR: An Oncogene in Human Cervical Cancer Interacting With MicroRNA-17-5p. (PMID: 28745272) Ji F … Du R (Oncology research 2018) 3 72
  3. Cav-1 promote lung cancer cell proliferation and invasion through lncRNA HOTAIR. (PMID: 29080835) Liu W … Nan KJ (Gene 2018) 3 72
  4. High expression of long non‑coding HOTAIR correlated with hepatocarcinogenesis and metastasis. (PMID: 29115524) Zhong DN … Tang W (Molecular medicine reports 2018) 3 72
  5. Knockdown of long non-coding RNA HOTAIR inhibits cisplatin resistance of gastric cancer cells through inhibiting the PI3K/Akt and Wnt/β-catenin signaling pathways by up-regulating miR-34a. (PMID: 29080815) Cheng C … Qin C (International journal of biological macromolecules 2018) 3 72

Products for HOTAIR Gene

Sources for HOTAIR Gene