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

HOXA-AS2 Gene

RNA gene   GIFtS: 21
GCID: GC07P027151

HOXA Cluster Antisense RNA 2

(Previous name: HOXA cluster antisense RNA 2 (non-protein coding))
  Search for HOXA-AS2
at  

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

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 11.2

Aliases
HOXA Cluster Antisense RNA 21 2
HOXA Cluster Antisense RNA 2 (Non-Protein Coding)1

External Ids:    HGNC: 437451   Entrez Gene: 2859432   Ensembl: ENSG000002535527   
ORGUL members:    fRNAdb10:FR198654 FR106866 FR015969 FR054497      
H-InvDB12:HIT000018844    
NCBI13:XR_000158 AK093987    
NONCODE14:n762 n764 n766 n369560 n767 see all 40      
Rfam:RF02138    
RNAdb15:LIT1581 EVF21469 EVF21467    

Export aliases for HOXA-AS2 gene to outside databases


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

GeneCards Summary for HOXA-AS2 Gene: 
HOXA-AS2 (HOXA cluster antisense RNA 2) is an RNA gene, and is affiliated with the lncRNA class.

fRNAdb sequence ontologies for HOXA-AS2 - the ORGUL cluster for this gene includes several descriptions:
-
antisense_RNA - Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for HOXA-AS2

(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NT_007819.17  NT_079592.2  NC_018918.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for HOXA-AS2
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for HOXA-AS2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HOXA-AS2


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

Entrez Gene cytogenetic band: 7p15.2   Ensembl cytogenetic band:  7p15.2   HGNC cytogenetic band: 7p15.2

HOXA-AS2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXA-AS2 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P027151:  view genomic region     (about GC identifiers)

Start:
27,147,396 bp from pter      End:
27,173,921 bp from pter
Size:
26,526 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 27,206,122-27,214,592     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for HOXA-AS2

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
LNCRNA: Long non-coding RNAs

  --

(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,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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(Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HOXA-AS2

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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
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Browse Tocris compounds for HOXA-AS2

Search CenterWatch for drugs/clinical trials and news about HOXA-AS2

(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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
2 fRNAdb Secondary structures:


Unigene Clusters for HOXA-AS2:

HOXA cluster antisense RNA 2
Hs.714774  [show with all ESTs], Hs.721126  [show with all ESTs]
Unigene Representative Sequences: XR_108755, BC035889
11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000518088 ENST00000522193 ENST00000517635 ENST00000518046 ENST00000593438
ENST00000523364(uc010kux.1) ENST00000517550(uc003syl.3) ENST00000517641
ENST00000521159 ENST00000521687 ENST00000524048
miRNA
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Additional mRNA sequence: BC035889.2 

6 DOTS entries:

DT.87046691  DT.99946118  DT.95295062  DT.40129211  DT.121115452  DT.91835260 

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™, 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 HOXA-AS2:RNAdb

HOXA-AS2 expression in normal human tissues (normalized intensities)      HOXA-AS2 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CGGGCGCCAA
HOXA-AS2 Expression
About this image


HOXA-AS2 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/9 selected tissues (see all 9) fully expand
 
 Uncategorized (Uncategorized)    fully expand to see all 3 entries
         PureStem Progenitor W10
 
 Smooth Muscle (Muscoskeletal System)
         Human Tracheal Smooth Muscle Cells (HTSMC)   
 
 Bone (Muscoskeletal System)
         Human Vertebral Mesenchymal Stem Cells (HVMSC)   
 
 Mesoderm (Gastrulation Derivatives)
         PureStem Z11, Meso Progenitor
 
 Lower Urinary Tract (Urinary System)
         Human Urothelial Cells (HUC)   

Genevestigator expression for HOXA-AS2

SOURCE GeneReport for Unigene clusters: Hs.714774 Hs.721126
    SABiosciences Custom PCR Arrays for HOXA-AS2
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXA-AS2

(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 HOXA-AS2 (if available)
TreeFam Gene Tree for HOXA-AS2 (if available)

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

(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) 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

10/202 SNPs in HOXA-AS2 are shown (see all 202)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 7 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1916317181,2
--27118900(+) ACTCGA/GAGTGT 1 -- us2k10--------
rs802875041,2
F--27119009(+) CGCCAT/CTCAGC 1 -- us2k11Minor allele frequency- C:0.01NA 120
rs359478681,2
C--27119078(+) GCTCAG/AGCTCC 1 -- us2k11Minor allele frequency- A:0.50NA 2
rs77987331,2
C,F,A--27119083(+) GGCTCC/G/TGACAC 1 -- us2k15WA NA EA 362
rs1821962281,2
--27119209(+) TCACCA/GCCGCG 1 -- us2k10--------
rs1861116871,2
--27119651(+) TCACGA/GAAGTC 1 -- us2k10--------
rs1498982201,2
C--27119718(+) GCTCTA/GTTTCT 1 -- us2k10--------
rs1898341311,2
--27119780(+) TGTGGA/GGTGAG 1 -- us2k10--------
rs1146783151,2
F--27119801(+) ACCAAG/CAAAAG 1 -- us2k11Minor allele frequency- C:0.04WA 118
rs592404631,2
C,F--27119828(+) TGCCCA/CGTTTA 1 -- us2k13Minor allele frequency- C:0.13CSA WA NA 240

HapMap Linkage Disequilibrium report for HOXA-AS2 (27147396 - 27173921 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for HOXA-AS2: --
SABiosciences Cancer Mutation PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HOXA-AS2
DNA2.0 Custom Variant and Variant Library Synthesis for HOXA-AS2

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

HOXA-AS2 for disorders           About MalaCards
OMIM information: 607530    

HOXA-AS2 for disorders           About GeneDecksing


Export disorders for HOXA-AS2 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)
About This Section

PubMed articles for HOXA-AS2 gene integrated from 9 sources:
(articles sorted by number of sources associating them with HOXA-AS2)
    Utopia: connect your pdf to the dynamic
world of online information

  1. HOX antisense lincRNA HOXA-AS2 is an apoptosis repress or in all Trans retinoic acid treated NB4 promyelocytic leukemia cells. (PubMed id 23649634)1, 3 Zhao H....Newburger P.E. (2013)
  2. 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. (2002)
  3. (PubMed id 12050232)10 
  4. (PubMed id 15608161)10 
  5. (PubMed id 17451645)10 
  6. (PubMed id 15103394)10 
  7. (PubMed id 18089548)10 
  8. (PubMed id 16628248)10 

(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)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 285943 HGNC: 43745 Ensembl:ENSG00000253552 euGenes: HUgn285943 ECgene: HOXA-AS2
H-InvDB: HOXA-AS2

(According to HUGE)
About This Section
  --

(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
  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for HOXA-AS2 gene:
Search GeneIP for patents involving HOXA-AS2

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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