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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HOTAIR Gene

RNA gene   GIFtS: 29
GCID: GC12M054356

HOX transcript antisense RNA

(Previous name: HOX transcript antisense RNA (non-protein coding) )
 Explore 4 diseases affiliated with
HOTAIR via
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Biological research products
for HOTAIR    

Aliases
for HOTAIR gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 3

Aliases
HOX Transcript Antisense RNA1 2
HOXC-AS41 2
HOXC11-AS11 2
NCRNA000721 2
HOX Transcript Antisense RNA (Non-Protein Coding)1
HOXAS2

External Ids:    HGNC: 335101   Entrez Gene: 1001247002   Ensembl: ENSG000002286307   OMIM: 6114005   
ORGUL members:         
NONCODE:n343067 n378191 n378970 n379007    

Export aliases for HOTAIR gene to outside databases

Previous GC identifers: GC00U922319 GC12U900912 GC12M052644 GC12M051393


Summaries
for HOTAIR gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for HOTAIR:
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)

Gene Wiki entry for HOTAIR


Genomic Views
for HOTAIR gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HOTAIR gene promoter:
         E2F-4   E2F-3a   E2F-1   E2F   FOXO1a   E2F-2   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HOTAIR


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q13.13   Ensembl cytogenetic band:  12q13.13   HGNC cytogenetic band: 12q13.13

HOTAIR Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOTAIR gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M054356:  view genomic region     (about GC identifiers)

Start:
 54,356,092 bp from pter      End:
 54,368,740 bp from pter
Size:
 12,649 bases      Orientation:
 minus strand
ORGUL member locations:
Legend (see complete legend)

  • n343067
  • n379007
  • n378191
  • n378970
54356095 54362413 54368731 chr12

Proteins
for HOTAIR gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB: --

Protein Domains /
Families
for HOTAIR gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Function
for HOTAIR gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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Inhib. RNA
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1 GenomeRNAi human phenotype for HOTAIR:
 Increased HPV18 LCR reporter a 


Pathways & Interactions
for HOTAIR gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HOTAIR

Drugs & Compounds
for HOTAIR gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for HOTAIR
Search CenterWatch for drugs/clinical trials and news about HOTAIR 

Transcripts
for HOTAIR gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Cluster for HOTAIR:

HOX transcript antisense RNA
Hs.197076  [show with all ESTs]
Unigene Representative Sequence: NR_047517
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000424518(uc009zne.3) ENST00000455246 ENST00000425595 ENST00000453875
ENST00000439545

miRNA
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Inhib. RNA
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Additional cDNA sequence: 

AK123741.1 DQ926657.1 NR_003716.3 NR_047517.1 NR_047518.1 

4 DOTS entries:

DT.40220113  DT.75160144  DT.121199151  DT.121199135 

GeneLoc Exon Structure


Expression
for HOTAIR gene

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

Expression evidence for HOTAIR:none

HOTAIR expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image

HOTAIR expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
Stem Cell Differentiation: 2 LifeMap Cells 
NameCategory
PureStem™ progenitor W8 (Embryonic Progenitor Cell)
CD31, CD144 positive cells (Two-step protocol fo...)
Expression: Positive    Negative     Selective marker
Experimental details: Curated     Microarrays     In-situ hybridization

Genevestigator expression for HOTAIR

SOURCE GeneReport for Unigene cluster: Hs.197076
    SABiosciences Custom PCR Arrays for HOTAIR
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In Situ
Assay Products: 
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Orthologs
for HOTAIR gene

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section
   --

ENSEMBL Gene Tree for HOTAIR (if available)
TreeFam Gene Tree for HOTAIR (if available) 

Paralogs
for HOTAIR gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

Genomic Variants
for HOTAIR gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/127 NCBI SNPs in HOTAIR are shown (see all 127)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 12 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs1849347871,2
--54355673(+) ACCAAA/GCACAG 3 -- ds50010--------
rs23661511,2
C,F,O,A,H,--54355708(+) AGCCCA/GTTGCC 3 -- ds500130Minor allele frequency- G:0.47NS EA NA CSA WA 2907
rs1181580901,2
C,F,--54356083(+) TTACAT/CANNNN 3 -- ds50011Minor allele frequency- C:0.03NA 120
rs1897794071,2
--54356090(+) CAGCAC/TGTATA 3 -- ds50010--------
rs1379954491,2
--54356106(+) CACATA/GTAAAA 3 -- nc-transcript-variant0--------
rs23661521,2
C,F,A,H,--54356389(+) ATTGCA/GTTCTT 3 -- nc-transcript-variant25Minor allele frequency- G:0.34NS EA NA WA CSA 2485
rs38399681,2
C,--54356452(-) CTGAAC/-TTCCT 3 -- nc-transcript-variant1Minor allele frequency- -:0.50NA 2
rs1997175841,2
C--54356452(+) AGGAAA/G/TTTCAG 6 -- nc-transcript-variant0--------
rs38399671,2
C--54356486(-) AAAAAC/-TCAGC 3 -- nc-transcript-variant2Minor allele frequency- -:0.25NA CSA 4
rs725199471,2
C,--54356486(+) TGCTG-/GRKTTT 3 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for HOTAIR (54356092 - 54368740 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for HOTAIR
     1 CNV: 3890

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Disorders / Diseases
for HOTAIR gene

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
HOTAIR for disorders           About GeneDecksing

OMIM gene information: 611400    OMIM disorders: --

4 diseases for HOTAIR:    About MalaCards
gastrointestinal stromal tumor    hepatocellular carcinoma    colorectal cancer    carcinoma


Export disorders for HOTAIR gene to outside databases

Publications
for HOTAIR gene

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for HOTAIR gene, integrated from 9 sources (see all 25):
(articles sorted by number of sources associating them with HOTAIR)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. (PubMed id 17604720)1, 3 Rinn J.L....Chang H.Y. (2007)
  2. HOTAIR lifts noncoding RNAs to new levels. (PubMed id 17604716)1, 3 Woo C.J. and Kingston R.E. (2007)
  3. Upregulation of miR-196a and HOTAIR drive malignant ch aracter in gastrointestinal stromal tumors. (PubMed id 22258453)1 Niinuma T....Shinomura Y. (2012)
  4. Intronic RNAs mediate EZH2 regulation of epigenetic ta rgets. (PubMed id 22659877)1 Guil S....Esteller M. (2012)
  5. Emerging Roles for Long Non-Coding RNAs in Cancer and Neurological Disorders. (PubMed id 22375145)1 Niland C.N....Khalil A.M. (2012)
  6. Mechanisms of long range silencing by imprinted macro non-coding RNAs. (PubMed id 22386265)1 Pauler F.M....Hudson Q.J. (2012)
  7. RNA-mediated silencing mechanisms in mammalian cells. (PubMed id 21507358)1 Wutz A. (2011)
  8. The sequence, structure and evolutionary features of H OTAIR in mammals. (PubMed id 21496275)1 He S....Zhu H. (2011)
  9. Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplant ation. (PubMed id 21327457)1 Yang Z....Zheng S.S. (2011)
  10. Deregulated HOX genes in ameloblastomas are located in physical contiguity to keratin genes. (PubMed id 21732412)1 Schiavo G....Cillo C. (2011)

External Searches for HOTAIR gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing HOTAIR gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 100124700 HGNC: 33510 Ensembl:ENSG00000228630 euGenes: HUgn100124700 ECgene: HOTAIR
H-InvDB: HOTAIR

Other Databases showing HOTAIR gene

(According to HUGE)
About This Section
   --

Specialized Databases showing HOTAIR gene

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for HOTAIR Pharmacogenomics, SNPs, Pathways

Intellectual Property
for HOTAIR gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for HOTAIR gene:
Search GeneIP for patents involving HOTAIR

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



Products
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