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HOTAIR Gene(RNA Gene)

HOX Transcript Antisense RNA

GCID:
GC12M053962
GIFtS:
31
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
  • 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 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 Pediculus Humanus Capitis Infestation and Pelvic Lipomatosis. Among its related pathways are LncRNA-mediated mechanisms of therapeutic resistance.

Gene Wiki entry 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

Regulatory Elements for HOTAIR Gene

Enhancers for HOTAIR Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12G053971 2.1 FANTOM5 Ensembl ENCODE dbSUPER 21.6 -15.3 -15287 36.8 CREB3L1 AGO1 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 ZNF263 SP3 ZNF740 MAP3K12 ENSG00000258344 LOC100652999 HOXC8 HOXC5 SP1 HOTAIR CBX5 HOXC4
GH12G053962 1.4 ENCODE dbSUPER 23.9 +8.3 8278 7.5 CREB3L1 DMAP1 FEZF1 YBX1 YY1 SLC30A9 ZNF143 ZNF263 MCM3 SP3 HOXC8 HOXC9 MAP3K12 HOXC5 HOTAIR HOXC6 HOXC4 SP1 SPRYD3 ENSG00000258086
GH12G054051 1.1 ENCODE 14.6 -78.6 -78562 4.8 HDGF PKNOX1 ARNT WRNIP1 SIN3A FEZF1 ZNF2 ZNF143 ZNF263 SP3 HOTAIR SP1 ENSG00000258344 HOXC4 HOXC5 HOXC6 MIR196A2 HOXC-AS3 HOXC10 HOXC8
GH12G054195 1.5 FANTOM5 Ensembl ENCODE 10.6 -221.7 -221720 3.1 HDGF PKNOX1 KLF17 ZNF121 GLIS2 ZNF366 SMARCC2 FOS KLF7 KDM4B MAP3K12 HOXC8 HOXC-AS1 HOXC-AS2 HOXC9 HOXC6 MIR196A2 MIR615 HOXC4 HOXC5
GH12G054191 1.2 Ensembl ENCODE 10.6 -216.8 -216782 0.9 ATF1 WRNIP1 ARID4B SIN3A ZNF2 ZNF143 KLF7 DEK SP3 YY2 HOXC8 HOXC-AS2 HOXC-AS1 HOXC9 HOXC6 MIR615 HOXC4 HOXC5 MAP3K12 LOC102724030
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HOTAIR on UCSC Golden Path with GeneCards custom track

Promoters for HOTAIR Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000052266 856 1001 AGO1 SIN3A FEZF1 GLIS2 DEK SP3 CAVIN1 REST SMARCB1 ZNF592

Transcription factor binding sites by QIAGEN in the HOTAIR gene promoter:

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 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
  7. Flow Cytometry

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

Flow Cytometry 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 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
  5. Flow Cytometry

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:

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
HOTAIR
ECgene alternative splicing isoforms for
HOTAIR

Expression for HOTAIR Gene

Products:

  1. Primer

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

Sequence variations from dbSNP and Humsavar for HOTAIR Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1000022974 -- 53,968,733(+) ATGTG(C/T)AGGCA nc-transcript-variant
rs1000147099 -- 53,966,109(+) CCGGC(C/T)GGGGA intron-variant
rs1000921625 -- 53,973,330(+) CGCCT(C/T)CAACC intron-variant
rs1000939554 -- 53,962,005(+) CCCAG(A/G)GTGGA downstream-variant-500B
rs1001149009 -- 53,968,418(+) CTGTT(G/T)ATGAC 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

Relevant External Links 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

(5) MalaCards diseases for HOTAIR Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pediculus humanus capitis infestation
  • head louse infestation
pelvic lipomatosis
  • excess of mature unencapsulated fatty tissue in the pelvis
lice infestation
  • infestation by pediculus
carotid artery dissection
  • dissection of carotid artery
retroperitoneum carcinoma
  • carcinoma of retroperitoneum
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for HOTAIR

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. HOTAIR lifts noncoding RNAs to new levels. (PMID: 17604716) Woo C.J. … Kingston R.E. (Cell 2007) 2 3 64
  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 64
  3. PRC2 is dispensable for HOTAIR-mediated transcriptional repression. (PMID: 28167697) Portoso M. … Margueron R. (EMBO J. 2017) 3 64
  4. HOTAIR rs920778 polymorphism is associated with ovarian cancer susceptibility and poor prognosis in a Chinese population. (PMID: 27690631) Qiu H. … Shi H. (Future Oncol 2017) 3 64
  5. The expression and significance of HOX transcript antisense RNA and epithelial-mesenchymal transition-related factors in esophageal squamous cell carcinoma. (PMID: 28260072) Da C. … Wang R. (Mol Med Rep 2017) 3 64

Products for HOTAIR Gene

Sources for HOTAIR Gene

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