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Aliases for HOTAIR Gene

Subcategory (RNA class) for HOTAIR Gene


Quality Score for this RNA gene is


Aliases for HOTAIR Gene

  • HOX Transcript Antisense RNA 2 3
  • 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

ORGUL Members 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 antisense 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

Genomic Location for HOTAIR Gene

53,962,308 bp from pter
53,974,956 bp from pter
12,649 bases
Minus strand

Genomic View for HOTAIR Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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 for HOTAIR Gene

Gene Families for HOTAIR Gene

  • LNCRNA :Long non-coding RNAs

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

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

Localization for HOTAIR Gene

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

Pathways for HOTAIR Gene

SuperPathways for HOTAIR Gene

No Data Available

Interacting Proteins for HOTAIR Gene

Gene Ontology (GO) - Biological Process for HOTAIR Gene


No data available for Pathways by source for HOTAIR Gene

Transcripts for HOTAIR Gene


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

Unigene Clusters for HOTAIR Gene

HOX transcript antisense RNA:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HOTAIR

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

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

No ASD Table

Relevant External Links for HOTAIR Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOTAIR Gene

mRNA expression in normal human tissues for HOTAIR Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Artery - Tibial (18.3), Skin - Sun Exposed (Lower leg) (6.6), and Testis (4.7).

SOURCE GeneReport for Unigene cluster for HOTAIR Gene Hs.197076

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

In Situ Assay Products

No data available for Protein differential expression in normal tissues , Protein expression , mRNA Expression by UniProt/SwissProt and Expression partners for HOTAIR Gene

Orthologs for HOTAIR Gene

Evolution for HOTAIR Gene

Gene Tree for HOTAIR (if available)
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 MAF
rs920777 -- 53,966,645(-) CCAGT(C/T)CCACC intron-variant
rs920778 -- 53,966,448(-) GAAAC(C/T)GTAAC intron-variant
rs1838169 -- 53,963,711(-) CCGGG(C/G)CTTCC nc-transcript-variant
rs1899663 -- 53,967,210(-) GTGGA(G/T)GTGAC intron-variant
rs2366151 -- 53,961,924(+) AGCCC(A/G)TTGCC downstream-variant-500B

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
Human Gene Mutation Database (HGMD)

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

Disorders for HOTAIR Gene

No disorders were found for HOTAIR Gene.

No data available for MalaCards , OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES , Novoseek inferred disease relationships , Genatlas and External Links 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
  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. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. (PMID: 19571010) Khalil A.M. … Rinn J.L. (Proc. Natl. Acad. Sci. U.S.A. 2009) 3
  4. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. (PMID: 20393566) Gupta R.A. … Chang H.Y. (Nature 2010) 3
  5. Long noncoding RNA as modular scaffold of histone modification complexes. (PMID: 20616235) Tsai M.C. … Chang H.Y. (Science 2010) 3

Products for HOTAIR Gene

Sources for HOTAIR Gene

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