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AGAP3 ArfGAP with GTPase domain, ankyrin repeat and PH domain 3 [ Homo sapiens (human) ]

Gene ID: 116988, updated on 5-Aug-2018

Summary

Official Symbol
AGAP3provided by HGNC
Official Full Name
ArfGAP with GTPase domain, ankyrin repeat and PH domain 3provided by HGNC
Primary source
HGNC:HGNC:16923
See related
Ensembl:ENSG00000133612 MIM:616813; Vega:OTTHUMG00000158724
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CRAG; AGAP-3; CENTG3; MRIP-1; cnt-g3
Summary
This gene encodes an essential component of the N-methyl-D-aspartate (NMDA) receptor signaling complex which mediates long-term potentiation in synapses by linking activation of NMDA receptor to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor trafficking. The encoded protein contains an N-terminal GTPase-like domain, a pleckstrin homology domain, an ArfGAP domain and several C-terminal ankryn repeat domains. [provided by RefSeq, Apr 2017]
Expression
Ubiquitous expression in brain (RPKM 17.1), lung (RPKM 9.1) and 25 other tissues See more
Orthologs

Genomic context

See AGAP3 in Genome Data Viewer
Location:
7q36.1
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (151085831..151144436)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (150782918..150841523)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene Fas activated serine/threonine kinase Neighboring gene uncharacterized LOC107986862 Neighboring gene transmembrane and ubiquitin like domain containing 1 Neighboring gene gastrulation brain homeobox 1 Neighboring gene ankyrin repeat and SOCS box containing 10

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ16146, FLJ34452

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTP binding IEA
Inferred from Electronic Annotation
more info
 
GTPase activator activity IEA
Inferred from Electronic Annotation
more info
 
GTPase activity ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
polyubiquitin modification-dependent protein binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
cellular response to reactive oxygen species ISO
Inferred from Sequence Orthology
more info
 
positive regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
 
protein import into nucleus, translocation ISO
Inferred from Sequence Orthology
more info
 
signal transduction IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell periphery ISO
Inferred from Sequence Orthology
more info
 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
membrane IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3
Names
CRAM-associated GTPase
CRMP (collapsin response mediator protein) associated
MR1-interacting protein
centaurin-gamma-3

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_053086.1 RefSeqGene

    Range
    5592..63606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001042535.3NP_001036000.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks several exons in the 3' coding region and includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (b) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AB209781, AC010973, BC044644
    Consensus CDS
    CCDS55185.1
    UniProtKB/Swiss-Prot
    Q96P47
    UniProtKB/TrEMBL
    Q86ST5
    Related
    ENSP00000418921.1, OTTHUMP00000213336, ENST00000473312.5, OTTHUMT00000351911
    Conserved Domains (2) summary
    cd04103
    Location:128285
    Centaurin_gamma; Centaurin gamma (CENTG) GTPase
    smart00010
    Location:126291
    small_GTPase; Small GTPase of the Ras superfamily; ill-defined subfamily
  2. NM_001281300.1NP_001268229.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform c

    See identical proteins and their annotated locations for NP_001268229.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks two alternate exons in the 3' coding region, and initiates translation from a downstream start codon, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AC010973, AK055393, BC048300, DA771207
    Consensus CDS
    CCDS64802.1
    UniProtKB/Swiss-Prot
    Q96P47
    UniProtKB/TrEMBL
    Q86XV5
    Related
    ENSP00000418016.1, OTTHUMP00000213334, ENST00000463381.5, OTTHUMT00000351909
    Conserved Domains (5) summary
    cd00204
    Location:458547
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:173314
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    sd00045
    Location:458488
    ANK; ANK repeat [structural motif]
    pfam01412
    Location:333447
    ArfGap; Putative GTPase activating protein for Arf
    cl21455
    Location:157
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
  3. NM_001308304.1NP_001295233.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several exons in the 3' coding region and includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (d) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC010973, BC044644, BC069236
    Consensus CDS
    CCDS83243.1
    UniProtKB/TrEMBL
    C9J975, Q86ST5
    Related
    ENSP00000418125.1, OTTHUMP00000213335, ENST00000479901.5, OTTHUMT00000351910
    Conserved Domains (2) summary
    cd04103
    Location:128285
    Centaurin_gamma; Centaurin gamma (CENTG) GTPase
    smart00010
    Location:126291
    small_GTPase; Small GTPase of the Ras superfamily; ill-defined subfamily
  4. NM_001308305.1NP_001295234.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, has multiple coding region differences, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (e) has distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AC010973, BC044644
    Consensus CDS
    CCDS78287.1
    UniProtKB/TrEMBL
    E7ESL9, Q86ST5
    Related
    ENSP00000335589.3, OTTHUMP00000213337, ENST00000335367.7, OTTHUMT00000351912
    Conserved Domains (2) summary
    cd04103
    Location:308465
    Centaurin_gamma; Centaurin gamma (CENTG) GTPase
    smart00010
    Location:306471
    small_GTPase; Small GTPase of the Ras superfamily; ill-defined subfamily
  5. NM_001350102.1NP_001337031.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform f

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks two alternate exons in the 3' coding region, compared to variant 1. The encoded isoform (f) is shorter than isoform a.
    Source sequence(s)
    AC010973, BC048300
    Conserved Domains (5) summary
    cd04103
    Location:128285
    Centaurin_gamma; Centaurin gamma (CENTG) GTPase
    cd00204
    Location:686775
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:401542
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    sd00045
    Location:686716
    ANK; ANK repeat [structural motif]
    pfam01412
    Location:561675
    ArfGap; Putative GTPase activating protein for Arf
  6. NM_001350103.1NP_001337032.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform g

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, contains an alternate internal exon, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (g) has a shorter and distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC010973, BC048300
    Conserved Domains (5) summary
    cd00204
    Location:443532
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:55299
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    sd00045
    Location:443473
    ANK; ANK repeat [structural motif]
    pfam01412
    Location:318432
    ArfGap; Putative GTPase activating protein for Arf
    cl26386
    Location:117319
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
  7. NM_001350104.1NP_001337033.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform h

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR, has multiple coding region differences, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (h) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC010973, BC048300
    Conserved Domains (4) summary
    cd00204
    Location:340429
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:55196
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    sd00045
    Location:340370
    ANK; ANK repeat [structural motif]
    pfam01412
    Location:215329
    ArfGap; Putative GTPase activating protein for Arf
  8. NM_031946.6NP_114152.3  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC010973, AF413079, BC048300
    Consensus CDS
    CCDS43681.1
    UniProtKB/Swiss-Prot
    Q96P47
    UniProtKB/TrEMBL
    Q86XV5
    Related
    ENSP00000380413.2, OTTHUMP00000213333, ENST00000397238.6, OTTHUMT00000351908
    Conserved Domains (8) summary
    cd04103
    Location:128285
    Centaurin_gamma; Centaurin gamma (CENTG) GTPase
    smart00010
    Location:126291
    small_GTPase; Small GTPase of the Ras superfamily; ill-defined subfamily
    cd00204
    Location:789878
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:401645
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    pfam00169
    Location:404465
    PH; PH domain
    pfam01412
    Location:664778
    ArfGap; Putative GTPase activating protein for Arf
    pfam12796
    Location:789879
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:789819
    ANK; ANK repeat [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p12 Primary Assembly

    Range
    151085831..151144436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011735.1XP_016867224.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X2

    Conserved Domains (4) summary
    cd00204
    Location:340429
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:55196
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    sd00045
    Location:340370
    ANK; ANK repeat [structural motif]
    pfam01412
    Location:215329
    ArfGap; Putative GTPase activating protein for Arf
  2. XM_011515780.2XP_011514082.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011514082.1

    UniProtKB/TrEMBL
    D3DX07
    Conserved Domains (7) summary
    cd00204
    Location:561650
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:173417
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    pfam00169
    Location:176237
    PH; PH domain
    pfam01412
    Location:436550
    ArfGap; Putative GTPase activating protein for Arf
    pfam12796
    Location:561651
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:561591
    ANK; ANK repeat [structural motif]
    cl21455
    Location:157
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
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