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AGAP4 Gene

protein-coding   GIFtS: 40
GCID: GC10M046322

ArfGAP With GTPase Domain, Ankyrin Repeat And PH Domain...

(Previous names: centaurin, gamma-like family, member 1)
(Previous symbol: CTGLF1)
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(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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Aliases
ArfGAP With GTPase Domain, Ankyrin Repeat And PH Domain 41 2     AGAP-42 3
CTGLF11 2 3     MRIP22 3
Centaurin, Gamma-Like Family, Member 11 2     ARF GTPase-Activating Protein2
Centaurin-Gamma-Like Family Member 12 3     Arf-GAP With GTPase, ANK Repeat And PH Domain-Containing Protein 42

External Ids:    HGNC: 234591   Entrez Gene: 1190162   Ensembl: ENSG000001882347   UniProtKB: Q96P643   

Export aliases for AGAP4 gene to outside databases

Previous GC identifers: GC10M045643 GC10M045375


(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 AGAP4 Gene:
AGAP4 (ArfGAP with GTPase domain, ankyrin repeat and PH domain 4) is a protein-coding gene. GO annotations related to this gene include phospholipid binding and ARF GTPase activator activity. An important paralog of this gene is AGAP5.

UniProtKB/Swiss-Prot: AGAP4_HUMAN, Q96P64
Function: Putative GTPase-activating protein (Potential)




(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 at NCBI GenBank:
NC_000010.10  NT_030059.14  NC_018921.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the AGAP4 gene promoter:
         AML1a   Tal-1beta   FOXL1   FOXJ2 (long isoform)   HFH-1   FOXJ2   Pax-4a   ITF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidAGAP4 promoter sequence
   Search Chromatin IP Primers for AGAP4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat AGAP4


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

Entrez Gene cytogenetic band: 10q11.22   Ensembl cytogenetic band:  10q11.22   HGNC cytogenetic band: 10q11.21

AGAP4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
AGAP4 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M046322:  view genomic region     (about GC identifiers)

Start:
46,321,042 bp from pter      End:
46,349,323 bp from pter
Size:
28,282 bases      Orientation:
minus strand

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: AGAP4_HUMAN, Q96P64 (See protein sequence)
Recommended Name: Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 4  
Size: 663 amino acids; 73070 Da
Miscellaneous: Encoded by one of the numerous copies of centaurin gamma-like genes clustered in the q11 region of
chromosome 10

Explore the universe of human proteins at neXtProt for AGAP4: NX_Q96P64

Explore proteomics data for AGAP4 at MOPED


See AGAP4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_597703.2  
ENSEMBL proteins: 
 ENSP00000392513   ENSP00000468160  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
PLEKH: Pleckstrin homology (PH) domain containing
ANKRD: Ankyrin repeat domain containing
ArfGAP: ADP-ribosylation factor GTPase activating proteins

5 InterPro protein domains:
 IPR001849 Pleckstrin_homology
 IPR001164 ArfGAP
 IPR011993 PH_like_dom
 IPR002110 Ankyrin_rpt
 IPR020683 Ankyrin_rpt-contain_dom

Graphical View of Domain Structure for InterPro Entry Q96P64

ProtoNet protein and cluster: Q96P64

3 Blocks protein domains:
IPB001164 HIV Rev interacting protein signature
IPB001849 Pleckstrin-like
IPB002110 Ankyrin repeat signature


UniProtKB/Swiss-Prot: AGAP4_HUMAN, Q96P64
Similarity: Belongs to the centaurin gamma-like family
Similarity: Contains 2 ANK repeats
Similarity: Contains 1 Arf-GAP domain
Similarity: Contains 1 PH domain


Find genes that share domains with AGAP4           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: AGAP4_HUMAN, Q96P64
Function: Putative GTPase-activating protein (Potential)

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
GO:0008060ARF GTPase activator activity IEA--
GO:0008270zinc ion binding IEA--
     
Find genes that share ontologies with AGAP4           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for AGAP4:
 Decreased influenza A/WSN/33 r 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for AGAP4

miRNA
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miRTarBase miRNAs that target AGAP4:
hsa-mir-1296-5p (MIRT036118)

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SwitchGear 3'UTR luciferase reporter plasmidAGAP4 3' UTR sequence
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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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol3
nucleus2
extracellular1
mitochondrion1

(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 AGAP4
Interactions:

    Search GeneGlobe Interaction Network for AGAP4

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

1 Interacting protein for AGAP4 (ENSP000003925134) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
USP19ENSP000003818634STRING: ENSP00000381863
About this table

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0032312regulation of ARF GTPase activity IEA--

Find genes that share ontologies with AGAP4           About GenesLikeMe



(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 compounds at ApexBio 

Browse Tocris compounds for AGAP4



(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for AGAP4 gene: 
NM_133446.2  

Unigene Cluster for AGAP4:

ArfGAP with GTPase domain, ankyrin repeat and PH domain 4
Hs.656384  [show with all ESTs]
Unigene Representative Sequence: AK096107
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000448048(uc001jcx.4 uc021pps.1 uc010qfl.2 uc001jcy.4)
ENST00000430779 ENST00000492347 ENST00000495243 ENST00000490752
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Additional mRNA sequence: 

AF411132.1 AK096107.1 BC048341.1 BC062366.1 BC171833.1 

17 DOTS entries:

DT.121289186  DT.95321258  DT.101979838  DT.445244  DT.92443635  DT.121288881  DT.437615  DT.100812744 
DT.95274220  DT.101973107  DT.102842747  DT.121222110  DT.121233727  DT.121280386  DT.121281807  DT.86856013 
DT.97796057 

Selected AceView cDNA sequences (see all 112):

AA370813 AF130105 CA950419 AI114519 AL045696 AL542342 BV177274 NM_133446 
BU567830 BV203153 BV202981 AW089174 CA424870 AF411132 BX111919 C00469 
BC051717 CB854530 BX506063 BX280268 AW019932 BV203150 BV200258 BV202983 

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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AGAP4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCCCGAGATG
AGAP4 Expression
About this image

AGAP4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

AGAP4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.656384
    Custom PCR Arrays for AGAP4
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for AGAP4

(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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This gene was present in the common ancestor of animals.

Orthologs for AGAP4 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
oppossum
(Monodelphis domestica)
Mammalia --
Uncharacterized protein
73(a)
1 → many
2(536230123-536278792)
chicken
(Gallus gallus)
Aves --
Uncharacterized protein
57(a)
1 → many
7(5139160-5321453)
lizard
(Anolis carolinensis)
Reptilia --
--
Uncharacterized protein
63(a)
10(a)
many ↔ many
many ↔ many
1(119629499-119789786)
1(119461547-119529618)
zebrafish
(Danio rerio)
Actinopterygii agap16
ArfGAP with GTPase domain, ankyrin repeat and PH d...
46(a)
1 → many
6(15964316-16312330) ENSDARG00000062123
fruit fly
(Drosophila melanogaster)
Insecta cenG1A6
centaurin gamma 1A
26(a)
1 → many
2L(13835567-13898715)
worm
(Caenorhabditis elegans)
Secernentea cnt-26
Protein CNT-2, isoform b
20(a)
1 → many
III(10655770-10677522) WBGene00000566


ENSEMBL Gene Tree for AGAP4 (if available)
TreeFam Gene Tree for AGAP4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for AGAP4 gene
LOC101060581  AGAP61 2  AGAP71 2  AGAP51 2  AGAP91 2  AGAP11  ASAP12  ARAP32  
ACAP22  ACAP32  ASAP22  ARAP12  AGAP32  ARAP22  AGAP22  AGAP12  
AGAP82  ACAP12  AGAP102  ASAP32  
Selected SIMAP similar genes for AGAP4 using alignment to 3 protein entries:     AGAP4_HUMAN (see all proteins) (see all similar genes):
AGAP8    AGAP6    AGAP7    CTGLF11P    AGAP5    AGAP10
AGAP11    AGAP9    FLJ00312    CENTG2    DKFZp761E2216    AGAP1
AGAP3    CCNYL2    CCNYL1    CCNY    CENTG3    AGAP2

Find genes that share paralogs with AGAP4           About GenesLikeMe



(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 AGAP4 (see all 90)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 10 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1997369631,2
C--46320981(+) TGGGGC/TGACAG 1 -- ds50010--------
rs1999765681,2
F--46321370(+) ACACAC/TACTTG 2 Y C mis11Minor allele frequency- T:0.00EU 1035
rs1447312481,2
F--46321387(+) CAGCCG/ATACTG 2 /Y syn11Minor allele frequency- A:0.01NA 4104
rs2011017651,2
F--46321406(+) CGTTGA/GTGCAC 2 T I mis11Minor allele frequency- G:0.00EU 1035
rs2000495501,2
F--46321527(+) CTTGCG/AGCAGG 2 /R /C mis11Minor allele frequency- A:0.19EU 309
rs2008371571,2
F--46321730(+) TCCACC/TGTTCC 2 Q R mis11Minor allele frequency- T:0.05EU 475
rs2016265451,2
F--46321748(+) CCCTCG/ATGGAC 2 /T /M mis11Minor allele frequency- A:0.02EU 531
rs2003537591,2
F--46321757(+) ACTTTT/ACTGAG 2 /E /V mis11Minor allele frequency- A:0.03EU 361
rs2016026201,2
C--46321761(+) TTCTGA/TGGTTT 2 T S mis11Minor allele frequency- T:0.00EU 569
rs2011793181,2
C,F--46321880(+) GCACAC/TGGGAA 2 H R mis11Minor allele frequency- T:0.05EU 1093

HapMap Linkage Disequilibrium report for AGAP4 (46321042 - 46349323 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for AGAP4 (see all 11):    About this table    
Variant IDTypeSubtypePubMed ID
nsv8630CNV Loss18304495
esv2750898CNV Loss17911159
esv34875CNV Gain17911159
nsv895114CNV Gain21882294
esv2750899CNV Gain17911159
nsv516485CNV Gain+Loss19592680
essv18092CNV CNV17122850
dgv253e1CNV Complex17122850
dgv254e1CNV Complex17122850
dgv251e1CNV Complex17122850

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing AGAP4
DNA2.0 Custom Variant and Variant Library Synthesis for AGAP4

(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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  --

(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 AGAP4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with AGAP4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  2. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (Sci Signal 2012)
  3. Genome-wide association study of hematological and biochemical traits in a Japanese population. (PubMed id 20139978)1 Kamatani Y....Kamatani N. (Nat. Genet. 2010)
  4. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)2 Deloukas P.... Rogers J. (Nature 2004)
  5. (PubMed id )2 

(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: 119016 HGNC: 23459 AceView: LOC439974 Ensembl:ENSG00000188234 euGenes: HUgn119016
ECgene: AGAP4 H-InvDB: AGAP4

(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 AGAP4 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 AGAP4 gene:
Search GeneIP for patents involving AGAP4

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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Biologicals
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 genOway: Develop your customized and physiologically relevant rodent model for AGAP4
 antibodies-online antibodies for AGAP4 (10 products)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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