Aliases for ARFGEF3 Gene

Aliases for ARFGEF3 Gene

  • ARFGEF Family Member 3 2 3 4 5
  • KIAA1244 2 3 4
  • BIG3 2 3 4
  • Brefeldin A-Inhibited Guanine Nucleotide-Exchange Protein 3 3 4
  • Protein Phosphatase 1, Regulatory Subunit 33 2 3
  • DJ171N11.1 2 3
  • C6orf92 3 4
  • PPP1R33 2 3
  • Chromosome 6 Open Reading Frame 92 2
  • ARFGEF3 5
  • A7322 3

External Ids for ARFGEF3 Gene

Previous HGNC Symbols for ARFGEF3 Gene

  • C6orf92
  • KIAA1244

Summaries for ARFGEF3 Gene

GeneCards Summary for ARFGEF3 Gene

ARFGEF3 (ARFGEF Family Member 3) is a Protein Coding gene. Diseases associated with ARFGEF3 include Hermansky-Pudlak Syndrome 3 and Granular Cell Carcinoma. Gene Ontology (GO) annotations related to this gene include binding and ARF guanyl-nucleotide exchange factor activity.

UniProtKB/Swiss-Prot Summary for ARFGEF3 Gene

  • Participates in the regulation of systemic glucose homeostasis, where it negatively regulates insulin granule biogenesis in pancreatic islet beta cells (By similarity). Also regulates glucagon granule production in pancreatic alpha cells (By similarity). Inhibits nuclear translocation of the transcriptional coregulator PHB2 and may enhance estrogen receptor alpha (ESR1) transcriptional activity in breast cancer cells (PubMed:19496786).

Additional gene information for ARFGEF3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ARFGEF3 Gene

Genomics for ARFGEF3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ARFGEF3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J138161 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +0.7 710 2.8 PRDM10 TFE3 KDM1A TARDBP FOXA1 PRDM1 ZIC2 RBFOX2 POLR2A IRF2 ARFGEF3 RF00017-5805 PBOV1
GH06J137214 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 5.2 -943.9 -943904 6.4 ZNF221 SP1 HNRNPL CREB1 GATAD2A ATF7 PRDM10 ZNF629 REST TFE3 IFNGR1 lnc-IFNGR1-1 lnc-SLC35D3-3 BCLAF1 MAP7 ARFGEF3 IL22RA2
GH06J138097 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 4.5 -58.3 -58277 12.5 ZNF221 RNF2 GATAD2A CTCF PRDM10 REST TFE3 ZNF692 RCOR2 JUND PERP HEBP2 ARFGEF3 lnc-ARFGEF3-1 HSALNG0053811 TNFAIP3
GH06J138229 Enhancer 1.2 Ensembl ENCODE dbSUPER 6.3 +69.8 69775 3.7 GATAD2A TFE3 NFKBIZ FOXA1 RFX1 POLR2A RXRB IRF2 GABPA CEBPA ARFGEF3 RF00017-5806 PBOV1 SMIM28
GH06J138226 Enhancer 1.2 Ensembl ENCODE dbSUPER 6.3 +65.5 65462 2.3 GATAD2A PRDM10 TFE3 NFKBIZ FOXA1 RXRB IRF2 SOX13 TAF1 RFX1 ARFGEF3 HEBP2 PBOV1 RF00017-5806 SMIM28
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ARFGEF3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ARFGEF3

Genomic Locations for ARFGEF3 Gene

Genomic Locations for ARFGEF3 Gene
chr6:138,161,690-138,344,663
(GRCh38/hg38)
Size:
182,974 bases
Orientation:
Plus strand
chr6:138,483,053-138,665,800
(GRCh37/hg19)
Size:
182,748 bases
Orientation:
Plus strand

Genomic View for ARFGEF3 Gene

Genes around ARFGEF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ARFGEF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ARFGEF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ARFGEF3 Gene

Proteins for ARFGEF3 Gene

  • Protein details for ARFGEF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5TH69-BIG3_HUMAN
    Recommended name:
    Brefeldin A-inhibited guanine nucleotide-exchange protein 3
    Protein Accession:
    Q5TH69
    Secondary Accessions:
    • C5NM88
    • Q76MU8
    • Q8N4Y4
    • Q96CH9
    • Q96P46
    • Q9ULH6

    Protein attributes for ARFGEF3 Gene

    Size:
    2177 amino acids
    Molecular mass:
    240652 Da
    Quaternary structure:
    • Interacts with PHB2.

neXtProt entry for ARFGEF3 Gene

Post-translational modifications for ARFGEF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ARFGEF3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ARFGEF3 Gene

Domains & Families for ARFGEF3 Gene

Protein Domains for ARFGEF3 Gene

Suggested Antigen Peptide Sequences for ARFGEF3 Gene

GenScript: Design optimal peptide antigens:
  • Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3_HUMAN)
genes like me logo Genes that share domains with ARFGEF3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for ARFGEF3 Gene

Function for ARFGEF3 Gene

Molecular function for ARFGEF3 Gene

UniProtKB/Swiss-Prot Function:
Participates in the regulation of systemic glucose homeostasis, where it negatively regulates insulin granule biogenesis in pancreatic islet beta cells (By similarity). Also regulates glucagon granule production in pancreatic alpha cells (By similarity). Inhibits nuclear translocation of the transcriptional coregulator PHB2 and may enhance estrogen receptor alpha (ESR1) transcriptional activity in breast cancer cells (PubMed:19496786).

Phenotypes From GWAS Catalog for ARFGEF3 Gene

Gene Ontology (GO) - Molecular Function for ARFGEF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IEA --
GO:0005086 ARF guanyl-nucleotide exchange factor activity IEA --
genes like me logo Genes that share ontologies with ARFGEF3: view
genes like me logo Genes that share phenotypes with ARFGEF3: view

Animal Models for ARFGEF3 Gene

MGI Knock Outs for ARFGEF3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ARFGEF3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ARFGEF3 Gene

Localization for ARFGEF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ARFGEF3 Gene

Cytoplasm. Cytoplasmic vesicle, secretory vesicle. Cytoplasmic vesicle, secretory vesicle membrane. Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ARFGEF3 gene
Compartment Confidence
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for ARFGEF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030133 transport vesicle IEA --
GO:0030658 transport vesicle membrane IEA --
genes like me logo Genes that share ontologies with ARFGEF3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ARFGEF3 Gene

Pathways & Interactions for ARFGEF3 Gene

PathCards logo

SuperPathways for ARFGEF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ARFGEF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010923 negative regulation of phosphatase activity IDA 19389623
GO:0030036 actin cytoskeleton organization IBA 21873635
GO:0032012 regulation of ARF protein signal transduction IEA --
genes like me logo Genes that share ontologies with ARFGEF3: view

No data available for Pathways by source and SIGNOR curated interactions for ARFGEF3 Gene

Drugs & Compounds for ARFGEF3 Gene

No Compound Related Data Available

Transcripts for ARFGEF3 Gene

mRNA/cDNA for ARFGEF3 Gene

1 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ARFGEF3

Alternative Splicing Database (ASD) splice patterns (SP) for ARFGEF3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: - - -
SP2: - -
SP3:

ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30
SP1:
SP2:
SP3:

Relevant External Links for ARFGEF3 Gene

GeneLoc Exon Structure for
ARFGEF3

Expression for ARFGEF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ARFGEF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ARFGEF3 Gene

This gene is overexpressed in Salivary gland (15.4), Cervix (10.4), Islet of Langerhans (10.1), Pancreas (8.1), and Lung (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ARFGEF3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ARFGEF3

mRNA Expression by UniProt/SwissProt for ARFGEF3 Gene:

Q5TH69-BIG3_HUMAN
Tissue specificity: Expressed in breast cancer cell lines. Not expressed in normal tissues such as duct, mammary gland, lung, heart, liver, kidnay, bone marrow.

Evidence on tissue expression from TISSUES for ARFGEF3 Gene

  • Nervous system(4.9)
  • Intestine(4.1)
  • Pancreas(3.1)
genes like me logo Genes that share expression patterns with ARFGEF3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for ARFGEF3 Gene

Orthologs for ARFGEF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ARFGEF3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia KIAA1244 30 31
  • 99.6 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia KIAA1244 31
  • 89 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia KIAA1244 30 31
  • 88.86 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia KIAA1244 30 31
  • 88.56 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia D10Bwg1379e 30 31
  • 86.54 (n)
OneToOne
Arfgef3 17
Platypus
(Ornithorhynchus anatinus)
Mammalia KIAA1244 31
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves KIAA1244 30 31
  • 77.73 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia KIAA1244 31
  • 84 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii KIAA1244 (1 of 2) 31
  • 77 (a)
OneToMany
si:ch211-71k24.5 31
  • 73 (a)
OneToMany
LOC562652 30
  • 69.32 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000635 30
  • 46.88 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG5937 30 31
  • 45.85 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea CELE_Y106G6G.2 30
  • 41.79 (n)
Y106G6G.2 31
  • 25 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 33 (a)
OneToOne
Species where no ortholog for ARFGEF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for ARFGEF3 Gene

ENSEMBL:
Gene Tree for ARFGEF3 (if available)
TreeFam:
Gene Tree for ARFGEF3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ARFGEF3: view image

Paralogs for ARFGEF3 Gene

(2) SIMAP similar genes for ARFGEF3 Gene using alignment to 1 proteins:

  • BIG3_HUMAN
genes like me logo Genes that share paralogs with ARFGEF3: view

No data available for Paralogs for ARFGEF3 Gene

Variants for ARFGEF3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ARFGEF3 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
713942 Benign: not provided 138,321,170(+) G/A MISSENSE_VARIANT
714321 Benign: not provided 138,262,830(+) T/G SYNONYMOUS_VARIANT
715845 Benign: not provided 138,210,011(+) C/T SYNONYMOUS_VARIANT
716072 Benign: not provided 138,317,246(+) T/C INTRON_VARIANT
718442 Benign: not provided 138,262,877(+) C/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for ARFGEF3 Gene

Structural Variations from Database of Genomic Variants (DGV) for ARFGEF3 Gene

Variant ID Type Subtype PubMed ID
esv2088282 CNV deletion 18987734
esv2672652 CNV deletion 23128226
esv2676513 CNV deletion 23128226
esv2732767 CNV deletion 23290073
esv2732768 CNV deletion 23290073
esv275052 CNV gain+loss 21479260
esv275212 CNV gain+loss 21479260
esv3610951 CNV loss 21293372
esv3610952 CNV loss 21293372
esv3610953 CNV loss 21293372
esv3610954 CNV loss 21293372
nsv5496 CNV deletion 18451855
nsv5497 CNV insertion 18451855
nsv823847 CNV gain 20364138

Variation tolerance for ARFGEF3 Gene

Residual Variation Intolerance Score: 1.42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.55; 88.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ARFGEF3 Gene

Human Gene Mutation Database (HGMD)
ARFGEF3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ARFGEF3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ARFGEF3 Gene

Disorders for ARFGEF3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for ARFGEF3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hermansky-pudlak syndrome 3
  • albinism with hemorrhagic diathesis and pigmented reticuloendothelial cells
granular cell carcinoma
  • granular cell adenocarcinoma
breast cancer
  • breast lobular carcinoma
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with ARFGEF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ARFGEF3 Gene

Publications for ARFGEF3 Gene

  1. Activation of an estrogen/estrogen receptor signaling by BIG3 through its inhibitory effect on nuclear transport of PHB2/REA in breast cancer. (PMID: 19496786) Kim JW … Katagiri T (Cancer science 2009) 3 4
  2. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10574462) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 3 4
  3. LMBR1L regulates lymphopoiesis through Wnt/β-catenin signaling. (PMID: 31073040) Choi JH … Beutler B (Science (New York, N.Y.) 2019) 3
  4. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. (PMID: 31091453) Shami Shah A … Baskin JM (Cell reports 2019) 3
  5. A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape. (PMID: 30833792) Hubel P … Pichlmair A (Nature immunology 2019) 3

Products for ARFGEF3 Gene

Sources for ARFGEF3 Gene