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AFAP1-AS1 Gene

RNA gene   GIFtS: 22
GCID: GC04P007756

AFAP1 Antisense RNA 1

(Previous names: AFAP1 antisense RNA (non-protein coding), AFAP1 antisense...)
(Previous symbols: AFAP1AS, AFAP1-AS)
  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
AFAP1 Antisense RNA 11 2
AFAP1-AS1 2
AFAP1AS1 2
AFAP1 Antisense RNA (Non-Protein Coding)1
AFAP1 Antisense RNA 1 (Non-Protein Coding)1

External Ids:    HGNC: 281411   Entrez Gene: 847402   Ensembl: ENSG000002726207   
ORGUL members:         

Export aliases for AFAP1-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 AFAP1-AS1 Gene:
AFAP1-AS1 (AFAP1 antisense RNA 1) is an RNA gene, and is affiliated with the antisense RNA class. Diseases associated with AFAP1-AS1 include barrett esophagus/esophageal adenocarcinoma, and barrett's esophagus.


(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_000004.12  NC_018915.2  NT_006051.19  
Regulatory elements:
   Search for regulatory transcription factor binding sites for AFAP1-AS1
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat AFAP1-AS1


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

Entrez Gene cytogenetic band: 4p16.1   Ensembl cytogenetic band:  4p16.1   HGNC cytogenetic band: 4p16.1

AFAP1-AS1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
AFAP1-AS1 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P007756:  view genomic region     (about GC identifiers)

Start:
7,755,817 bp from pter      End:
7,780,655 bp from pter
Size:
24,839 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for AFAP1-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, and/or Cloud-Clone Corp.)
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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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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,
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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Phenotypes:
     1 GenomeRNAi human phenotype for AFAP1-AS1:
 Decreased POU5F1-GFP protein e 

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 AFAP1-AS1
Interactions:

    Search GeneGlobe Interaction Network for AFAP1-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 Tocris compounds for AFAP1-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,
Conferences by KenesGroup, 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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REFSEQ mRNAs for AFAP1-AS1 gene: 
NM_032654.1  

Unigene Cluster for AFAP1-AS1:

AFAP1 antisense RNA 1
Hs.663029  [show with all ESTs]
Unigene Representative Sequence: BC043614
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000608442(antisense)
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Additional mRNA sequence: 

BC004397.1 BC014113.1 BC043614.2 

3 DOTS entries:

DT.40122396  DT.40199596  DT.100746208 

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 AFAP1-AS1:none

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

AFAP1-AS1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.663029
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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 AFAP1-AS1 (if available)
TreeFam Gene Tree for AFAP1-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 AFAP1-AS1 (see all 180)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 4 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1440935671,2
--7753992(+) TGTTAC/TAAATT 1 -- us2k10--------
rs558965501,2
C--7754006(+) GCCAGG/AACCAT 1 -- us2k15Minor allele frequency- A:0.13WA NA EA 362
rs571024841,2
C,F--7754008(+) CAGGAC/TCATGC 1 -- us2k12Minor allele frequency- T:0.06WA 120
rs1857155261,2
--7754036(+) CCCCCC/TGTATT 1 -- us2k10--------
rs1487032031,2
--7754109(+) TTCTCA/GGTGAC 1 -- us2k10--------
rs1912881751,2
--7754158(+) TCTTTA/GTTTCT 1 -- us2k10--------
rs1421615251,2
C--7754178(+) TTGTGC/TAGATC 1 -- us2k10--------
rs1467366621,2
C--7754181(+) TGCAGA/GTCAAG 1 -- us2k10--------
rs353843191,2
C,F--7754223(+) AATCCC/GAGAGA 1 -- us2k14Minor allele frequency- G:0.18NA CSA EA 244
rs1412872881,2
--7754270(+) GTTCAA/GCCATG 1 -- us2k10--------

HapMap Linkage Disequilibrium report for AFAP1-AS1 (7755817 - 7780655 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for AFAP1-AS1 (see all 11):    About this table    
Variant IDTypeSubtypePubMed ID
esv2727075CNV Deletion23290073
esv2727076CNV Deletion23290073
esv2727074CNV Deletion23290073
esv2727078CNV Deletion23290073
esv2727077CNV Deletion23290073
esv2727079CNV Deletion23290073
nsv878577CNV Loss21882294
nsv878575CNV Loss21882294
nsv878570CNV Gain21882294
nsv822468CNV Gain20364138

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing AFAP1-AS1
DNA2.0 Custom Variant and Variant Library Synthesis for AFAP1-AS1

(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.)
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4 diseases for AFAP1-AS1:    
About MalaCards
barrett esophagus/esophageal adenocarcinoma    barrett's esophagus    esophagitis    adenocarcinoma


AFAP1-AS1 for disorders           About GeneDecksing


Export disorders for AFAP1-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 AFAP1-AS1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with AFAP1-AS1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett's esophagus and esophageal adenocarcinoma. (PubMed id 23333711)1, 3 Wu W....Meltzer S.J. (Gastroenterology 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. (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: 84740 HGNC: 28141 Ensembl:ENSG00000272620 euGenes: HUgn84740 ECgene: AFAP1-AS1
H-InvDB: AFAP1-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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NameDescription
PharmGKB entry for AFAP1-AS1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for AFAP1-AS1 gene:
Search GeneIP for patents involving AFAP1-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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