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    ARFGEF3 ARFGEF family member 3 [ Homo sapiens (human) ]

    Gene ID: 57221, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ARFGEF3provided by HGNC
    Official Full Name
    ARFGEF family member 3provided by HGNC
    Primary source
    HGNC:HGNC:21213
    See related
    Ensembl:ENSG00000112379 MIM:617411; AllianceGenome:HGNC:21213
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BIG3; A7322; C6orf92; PPP1R33; KIAA1244; dJ171N11.1
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of ARF protein signal transduction. Predicted to be located in Golgi apparatus and transport vesicle membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 10.4), prostate (RPKM 8.3) and 15 other tissues See more
    Orthologs
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    Genomic context

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    See ARFGEF3 in Genome Data Viewer
    Location:
    6q23.3-q24.1
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (138161939..138344663)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (139350430..139533149)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (138483076..138665800)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378021 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90506 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:138408219-138409418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17593 Neighboring gene p53 apoptosis effector related to PMP22 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:138482885-138483855 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90516 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90526 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:138504387-138504888 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:138504889-138505388 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90581 Neighboring gene prostate and breast cancer overexpressed 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:138608085-138608584 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:138650317-138651290 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:138651291-138652264 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:138652315-138653064 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:138653065-138653812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:138655517-138656120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:138656121-138656722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:138698741-138699245 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:138724054-138724574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17595 Neighboring gene small integral membrane protein 28 Neighboring gene MARCKS like 1 pseudogene 2 Neighboring gene heme binding protein 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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 Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Biophysical characterization of the breast cancer-related BIG3-PHB2 interaction: Effect of non-conserved loop region of BIG3 on the structure and the interaction. Chigira T, et al. Biochem Biophys Res Commun, 2019 Oct 8. PMID 31421830
    2. Brefeldin A-inhibited guanine nucleotide exchange protein 3 is localized in lysosomes and regulates GABA signaling in hippocampal neurons. Liu T, et al. J Neurochem, 2016 Dec. PMID 27696409
    3. Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure. Chen YA, et al. BMC Res Notes, 2014 Jul 6. PMID 24997568, Free PMC Article
    4. The survival and proliferation of osteosarcoma cells are dependent on the mitochondrial BIG3-PHB2 complex formation. Toki S, et al. Cancer Sci, 2021 Oct. PMID 34363714, Free PMC Article
    5. Activation of an estrogen/estrogen receptor signaling by BIG3 through its inhibitory effect on nuclear transport of PHB2/REA in breast cancer. Kim JW, et al. Cancer Sci, 2009 Aug. PMID 19496786, Free PMC Article

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The survival and proliferation of osteosarcoma cells are dependent on the mitochondrial BIG3-PHB2 complex formation.
      Title: The survival and proliferation of osteosarcoma cells are dependent on the mitochondrial BIG3-PHB2 complex formation.
    2. These results establish a model for the BIG3-PHB2 interaction and an entry for drug discovery for breast cancer.
      Title: Biophysical characterization of the breast cancer-related BIG3-PHB2 interaction: Effect of non-conserved loop region of BIG3 on the structure and the interaction.
    3. BIG3 (ARFGEF3) is predicted to interact with its partner PHB2 through an ARM-type alpha-helical structure.
      Title: Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ32064, KIAA1244

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of ARF protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in transport vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    brefeldin A-inhibited guanine nucleotide-exchange protein 3
    Names
    protein phosphatase 1, regulatory subunit 33

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_020340.5 → NP_065073.3  brefeldin A-inhibited guanine nucleotide-exchange protein 3

      See identical proteins and their annotated locations for NP_065073.3

      Status: VALIDATED

      Source sequence(s)
      AB252196, BU682567
      Consensus CDS
      CCDS5189.2
      UniProtKB/Swiss-Prot
      C5NM88, Q5TH69, Q76MU8, Q8N4Y4, Q96CH9, Q96P46, Q9ULH6
      UniProtKB/TrEMBL
      B5MDV5
      Related
      ENSP00000251691.4, ENST00000251691.5
      Conserved Domains (4) summary
      smart00222
      Location:586 → 798
      Sec7; Sec7 domain
      pfam03426
      Location:1976 → 2055
      CBM_15; Carbohydrate binding domain (family 15)
      pfam09324
      Location:1246 → 1303
      DUF1981; Domain of unknown function (DUF1981)
      pfam16213
      Location:5 → 168
      DCB; Dimerization and cyclophilin-binding domain of Mon2

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      138161939..138344663
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419108.1 → XP_047275064.1  brefeldin A-inhibited guanine nucleotide-exchange protein 3 isoform X1

    RNA

    1. XR_001743524.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      139350430..139533149
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355992.1 → XP_054211967.1  brefeldin A-inhibited guanine nucleotide-exchange protein 3 isoform X1

    RNA

    1. XR_008487366.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5TH69.3 GenPept UniProtKB/Swiss-Prot:Q5TH69

    Gene LinkOut

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