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HOTAIR Gene(RNA Gene)

HOX Transcript Antisense RNA

GCID:
GC12M053962
GIFtS:
23
Genes Participants
UDN Logo

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
  • HOX Transcript Antisense RNA (Non-Protein Coding) 2 3
  • HOXC Cluster Antisense RNA 4 (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 the HOXC genes. It functions through an RNA product, which binds lysine specific demethylase 1 (LSD1) and Polycomb repressive complex 2 (PRC2), and servers 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, Mar 2017]

GeneCards Summary for HOTAIR Gene

HOTAIR (HOX Transcript Antisense RNA) is an RNA Gene, and is affiliated with the non-coding RNA class. Diseases associated with HOTAIR include Gastric Cardia Adenocarcinoma and Gastrointestinal System Cancer. Among its related pathways are LncRNA-mediated mechanisms of therapeutic resistance.

Gene Wiki entry for HOTAIR Gene

Additional gene information for HOTAIR Gene

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

Genomics for HOTAIR Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for HOTAIR Gene

Promoters and enhancers for HOTAIR Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH12J053971 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 21.6 -15.3 -15287 36.8 FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF416 ZNF143 ZNF548 SP3 NFYC HOXC8 HOXC5 HOXC11 HOXC9 HOXC6 HOXC10 GC12P054010 GC12P054063 MIR196A2 HNRNPA1
GH12J053962 Promoter/Enhancer 1.6 EPDnew ENCODE dbSUPER 23.9 +8.3 8278 7.5 PKNOX1 ZNF133 SIN3A FEZF1 ZNF2 GLIS2 DEK SP3 REST ZNF610 ENSG00000274817 ENSG00000277129 ENSG00000277994 HOXC11 HOTAIR MAP3K12 HOXC6 MIR196A2 HOXC5 HOXC13
GH12J054051 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 14.6 -78.6 -78561 4.8 HDGF PKNOX1 SMAD1 ARNT FEZF1 ZNF2 YY1 ZNF213 ZNF143 SP3 HOXC4 AAAS ATF7 RARG HNRNPA1 ENSG00000260470 LOC105378250 PCBP2 SP1 HOTAIR
GH12J054188 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10.7 -213.9 -213857 1.6 PKNOX1 ARNT ARID4B SIN3A ETS1 ZNF766 GLIS2 ZNF213 E2F8 ELK1 LOC105369777 SMUG1 FLJ12825 HOXC8 HOXC-AS1 HOXC-AS2 HOXC9 HOXC6 ENSG00000257605 MIR615
GH12J054079 Promoter/Enhancer 1.4 Ensembl ENCODE 10.4 -106.3 -106333 4.6 HDGF PKNOX1 FEZF1 GLI4 ZNF2 YY1 ZNF121 GLIS2 ZNF213 ZFP91 LOC100240734 LOC100240735 SMUG1 FLJ12825 CBX5 MIR615 HOXC4 HOXC5 HOXC6 HOXC8
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for HOTAIR Gene

Genomic Locations for HOTAIR Gene
chr12:53,962,308-53,974,956
(GRCh38/hg38)
Size:
12,649 bases
Orientation:
Minus strand
chr12:54,356,092-54,368,740
(GRCh37/hg19)
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 Structure • Gene Density

RefSeq DNA sequence for HOTAIR Gene

Proteins for HOTAIR Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

HGNC:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes From GWAS Catalog for HOTAIR Gene

Phenotypes for HOTAIR Gene

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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOTAIR

Clone Products

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
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 2
extracellular 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

Interacting Proteins for HOTAIR Gene

Gene Ontology (GO) - Biological Process for HOTAIR Gene

None

No data available for SIGNOR curated interactions for HOTAIR Gene

Drugs & Compounds for HOTAIR Gene

Products:

  1. Drug

(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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for HOTAIR Gene

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

Unigene Clusters for HOTAIR Gene

HOX transcript antisense RNA:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOTAIR

Clone Products

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

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for HOTAIR Gene
mRNA expression by GTEx 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).

NURSA nuclear receptor signaling pathways regulating expression of HOTAIR Gene:

HOTAIR

SOURCE GeneReport for Unigene cluster for HOTAIR Gene:

Hs.197076
genes like me logo Genes that share expression patterns with HOTAIR: view

Primer Products

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 , Evidence on tissue expression from TISSUES 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)

No data available for Orthologs for HOTAIR Gene

Paralogs for HOTAIR Gene

No data available for Paralogs for HOTAIR Gene

Variants for HOTAIR Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for HOTAIR Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000022974 -- 53,968,733(-) C/T non_coding_transcript_variant
rs1000147099 -- 53,966,109(-) C/T intron_variant
rs1000921625 -- 53,973,330(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000939554 -- 53,962,005(-) A/G downstream_transcript_variant
rs1001149009 -- 53,968,418(-) T/G intron_variant

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

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

Disorders for HOTAIR Gene

MalaCards: The human disease database

(69) MalaCards diseases for HOTAIR Gene - From: LncRNADisease, HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
gastric cardia adenocarcinoma
  • adenocarcinoma of cardia of stomach
gastrointestinal system cancer
  • digestive system cancer
cerebrovascular disease
  • cerebrovascular accident
lemierre's syndrome
  • acute sore throat
functionless pituitary adenoma
  • non-functioning neoplasm of the pituitary
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HOTAIR

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. (PMID: 17604720) Rinn JL … Chang HY (Cell 2007) 2 3 58
  2. HOTAIR lifts noncoding RNAs to new levels. (PMID: 17604716) Woo CJ … Kingston RE (Cell 2007) 2 3 58
  3. Cav-1 promote lung cancer cell proliferation and invasion through lncRNA HOTAIR. (PMID: 29080835) Liu W … Nan KJ (Gene 2018) 3 58
  4. Serum HOTAIR and GAS5 levels as predictors of survival in patients with glioblastoma. (PMID: 28926136) Shen J … Zhao H (Molecular carcinogenesis 2018) 3 58
  5. Long non-coding RNA HOTAIR and STAT3 synergistically regulate the cervical cancer cell migration and invasion. (PMID: 29572071) Zhang Y … Jin Z (Chemico-biological interactions 2018) 3 58

Products for HOTAIR Gene

Sources for HOTAIR Gene

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