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Aliases for HOTAIR Gene

Subcategory (RNA class) for HOTAIR Gene

non-coding RNA

Quality Score for this RNA gene is

13

Aliases for HOTAIR Gene

  • HOX Transcript Antisense RNA 2 3 5
  • HOXC Cluster Antisense RNA 4 (Non-Protein Coding) 2 3
  • HOX Transcript Antisense RNA (Non-Protein Coding) 2 3
  • Hox Transcript Antisense Intergenic RNA 3
  • Non-Protein Coding RNA 72 2
  • HOXC11-AS1 3
  • NCRNA00072 3
  • HOXC-AS4 3
  • HOXAS 3

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 HOXC genes. It represses transcription of HOXD genes on chromosome 2 in trans. This gene is shuttled from chromosome 12 to chromosome 2 by a component of Polycomb Repressive Complex 2 (PRC2). This gene interacts with both PRC2 and lysine specific demethylase 1 (LSD1) complexes through its 5' and 3' domains, respectively, and serves as a scaffold to assemble PRC2 and LSD1 complexes to the HOXD gene cluster. It couples H3K27 methylation and H3K4 demethylation for epigenetic silencing of HOXD genes in multiple tissues. This gene is highly expressed in multiple tumors. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Feb 2013]

GeneCards Summary for HOTAIR Gene

HOTAIR (HOX Transcript Antisense RNA) is an RNA Gene, and is affiliated with the non-coding RNA class.

Gene Wiki entry for HOTAIR Gene

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

Genomics for HOTAIR Gene

Regulatory Elements for HOTAIR Gene

Promoters for HOTAIR Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HOTAIR on UCSC Golden Path with GeneCards custom track

Genomic Location for HOTAIR Gene

Chromosome:
12
Start:
53,962,308 bp from pter
End:
53,974,956 bp from pter
Size:
12,649 bases
Orientation:
Minus strand

Genomic View for HOTAIR Gene

Genes around HOTAIR on UCSC Golden Path with GeneCards custom track

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

Graphical View of Domain Structure for InterPro Entry

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

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for HOTAIR Gene

Function for HOTAIR Gene

Phenotypes for HOTAIR Gene

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

miRNA for HOTAIR Gene

miRTarBase miRNAs that target HOTAIR

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

Localization for HOTAIR Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HOTAIR Gene COMPARTMENTS Subcellular localization image for HOTAIR gene
Compartment Confidence
nucleus 2

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for HOTAIR Gene

Pathways & Interactions for HOTAIR Gene

SuperPathways for HOTAIR Gene

No Data Available

Interacting Proteins for HOTAIR Gene

Gene Ontology (GO) - Biological Process for HOTAIR Gene

None

No data available for Pathways by source 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

mRNA/cDNA for HOTAIR Gene

(5) Additional mRNA sequences :
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HOTAIR Gene

HOX transcript antisense RNA:
Representative Sequences:

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

No ASD Table

Relevant External Links for HOTAIR Gene

GeneLoc Exon Structure for
HOTAIR
ECgene alternative splicing isoforms for
HOTAIR

Expression for HOTAIR Gene

mRNA expression in normal human tissues 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).

SOURCE GeneReport for Unigene cluster for HOTAIR Gene Hs.197076

genes like me logo Genes that share expression patterns with HOTAIR: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners 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)

No data available for Orthologs for HOTAIR Gene

Paralogs for HOTAIR Gene

No data available for Paralogs for HOTAIR Gene

Variants for HOTAIR Gene

Sequence variations from dbSNP and Humsavar for HOTAIR Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1838169 -- 53,963,711(-) CCGGG(C/G)CTTCC nc-transcript-variant
rs2366151 -- 53,961,924(+) AGCCC(A/G)TTGCC downstream-variant-500B
rs2366152 -- 53,962,605(+) ATTGC(A/G)TTCTT nc-transcript-variant
rs4511324 -- 53,971,751(-) CTGGG(C/T)CCAAG intron-variant
rs4759314 -- 53,968,051(+) GGCCA(A/G)GCGGA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv826379 CNV Gain 20364138
nsv899100 CNV Loss 21882294
dgv512e1 CNV Complex 17122850
nsv428282 CNV Gain 18775914

Relevant External Links for HOTAIR Gene

HapMap Linkage Disequilibrium report
HOTAIR
Human Gene Mutation Database (HGMD)
HOTAIR

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for HOTAIR Gene

Disorders for HOTAIR Gene

Relevant External Links for HOTAIR

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HOTAIR

No disorders were found for HOTAIR Gene.

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

Publications for HOTAIR Gene

  1. HOTAIR lifts noncoding RNAs to new levels. (PMID: 17604716) Woo C.J. … Kingston R.E. (Cell 2007) 2 3 67
  2. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. (PMID: 17604720) Rinn J.L. … Chang H.Y. (Cell 2007) 2 3
  3. Long non-coding RNA HOTAIR modulates c-KIT expression through sponging miR-193a in acute myeloid leukemia. (PMID: 25979172) Xing C.Y. … Gao S.M. (FEBS Lett. 2015) 3
  4. Long non-coding RNA HOTAIR promotes tumor cell invasion and metastasis by recruiting EZH2 and repressing E-cadherin in oral squamous cell carcinoma. (PMID: 25901533) Wu Y. … Hao X. (Int. J. Oncol. 2015) 3
  5. HOTAIR forms an intricate and modular secondary structure. (PMID: 25866246) Somarowthu S. … Pyle A.M. (Mol. Cell 2015) 3

Products for HOTAIR Gene

Sources for HOTAIR Gene

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