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HOXD-AS1 Gene

RNA gene   GIFtS: 19
GCID: GC02M177039

HOXD Cluster Antisense RNA 1

(Previous name: HOXD cluster antisense RNA 1 (non-protein coding))
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): antisense

Quality score for this RNA gene is 3

Aliases
HOXD Cluster Antisense RNA 11 2
HOXD Cluster Antisense RNA 1 (Non-Protein Coding)1
Mdgt2

External Ids:    HGNC: 437551   Entrez Gene: 4010222   Ensembl: ENSG000002241897   
ORGUL members:         

Export aliases for HOXD-AS1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HOXD-AS1 Gene:
HOXD-AS1 (HOXD cluster antisense RNA 1) is an RNA gene, and is affiliated with the antisense RNA class. Diseases associated with HOXD-AS1 include intrahepatic cholangiocarcinoma, and cholangiocarcinoma.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000002.12  NC_018913.2  NT_005403.18  
Regulatory elements:
   Search for regulatory transcription factor binding sites for HOXD-AS1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HOXD-AS1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HOXD-AS1


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

Entrez Gene cytogenetic band: 2q31.2   Ensembl cytogenetic band:  2q31.1   HGNC cytogenetic band: 2q31.1

HOXD-AS1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXD-AS1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M177039:  view genomic region     (about GC identifiers)

Start:
177,037,923 bp from pter      End:
177,053,686 bp from pter
Size:
15,764 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for HOXD-AS1

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HOXD-AS1
Interactions:

    Search GeneGlobe Interaction Network for HOXD-AS1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for HOXD-AS1



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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Unigene Cluster for HOXD-AS1:

HOXD cluster antisense RNA 1
Hs.98661  [show with all ESTs]
Unigene Representative Sequence: BC047481
12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000416928(antisense) ENST00000417086(antisense) ENST00000547207(antisense) ENST00000436126(antisense) ENST00000447538(antisense)
ENST00000549329(antisense) ENST00000546798(antisense) ENST00000413969(antisense) ENST00000552156(antisense) ENST00000456876(antisense)
ENST00000425005(antisense) ENST00000452365(antisense)
miRNA
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Additional mRNA sequence: 

BC030713.2 BC047481.1 NR_033979.1 

7 DOTS entries:

DT.441393  DT.75180382  DT.110204  DT.100644759  DT.120952682  DT.120952683  DT.75182861 

GeneLoc Exon Structure


(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for HOXD-AS1:none

HOXD-AS1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
HOXD-AS1 Expression
About this image

HOXD-AS1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.98661
    Custom PCR Arrays for HOXD-AS1
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In Situ
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(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)
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ENSEMBL Gene Tree for HOXD-AS1 (if available)
TreeFam Gene Tree for HOXD-AS1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for HOXD-AS1 (see all 206)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1508715121,2
--177038441(+) GTTTAC/TTCCTG 1 -- nc-transcript-variant0--------
rs1401185221,2
C--177038530(+) GTGGAC/TAACTT 1 -- nc-transcript-variant0--------
rs1497364911,2
C--177038605(+) TCAGC-/AAAAGTC 1 -- nc-transcript-variant0--------
rs2018416131,2
--177038617(+) GCCCA-/CGCATC 1 -- nc-transcript-variant0--------
rs1441986231,2
C--177038762(+) TTCAC-/TAAG  
        
TAATG
1 -- nc-transcript-variant0--------
rs14759701,2
C,F,A--177039009(+) GAATTT/CCTAAT 1 -- nc-transcript-variant2Minor allele frequency- C:0.21MN NA 304
rs15493341,2
C,F,A--177039197(-) CATTAT/CGTATT 1 -- nc-transcript-variant12Minor allele frequency- C:0.27MN NA WA CSA EA 556
rs64335711,2
C,A--177039578(+) AGCCGT/GGGGAG 1 -- nc-transcript-variant8Minor allele frequency- G:0.20WA NA CSA 248
rs1439081061,2
--177039660(+) AATTAG/TAAACA 1 -- nc-transcript-variant0--------
rs1472848811,2
--177039686(+) CGCAAC/TAAATT 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for HOXD-AS1 (177037923 - 177053686 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for HOXD-AS1: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HOXD-AS1
DNA2.0 Custom Variant and Variant Library Synthesis for HOXD-AS1

(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.)
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3 diseases for HOXD-AS1:    
About MalaCards
intrahepatic cholangiocarcinoma    cholangiocarcinoma    ovarian cancer


HOXD-AS1 for disorders           About GeneDecksing


Export disorders for HOXD-AS1 gene to outside databases

(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)
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PubMed articles for HOXD-AS1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with HOXD-AS1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells. (PubMed id 24555823)1, 3 Batagov A.O....Kurochkin I.V. (BMC Syst Biol 2013)
  2. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. (PubMed id 24381249)1, 3 Sauvageau M....Rinn J.L. (Elife 2013)
  3. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. (PubMed id 23535730)1 Pharoah P.D....Sellers T.A. (Nat. Genet. 2013)
  4. A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. (PubMed id 20852632)1 Goode E.L....Pharoah P.D. (Nat. Genet. 2010)
  5. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (Biochem. Biophys. Res. Commun. 2006)
  6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 401022 HGNC: 43755 Ensembl:ENSG00000224189 euGenes: HUgn401022 ECgene: HOXD-AS1
H-InvDB: HOXD-AS1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HOXD-AS1 gene:
Search GeneIP for patents involving HOXD-AS1

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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