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    ARFGEF1 ARF guanine nucleotide exchange factor 1 [ Homo sapiens (human) ]

    Gene ID: 10565, updated on 3-Nov-2024

    Summary

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    Official Symbol
    ARFGEF1provided by HGNC
    Official Full Name
    ARF guanine nucleotide exchange factor 1provided by HGNC
    Primary source
    HGNC:HGNC:15772
    See related
    Ensembl:ENSG00000066777 MIM:604141; AllianceGenome:HGNC:15772
    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
    BIG1; P200; DEDISB; ARFGEP1
    Summary
    ADP-ribosylation factors (ARFs) play an important role in intracellular vesicular trafficking. The protein encoded by this gene is involved in the activation of ARFs by accelerating replacement of bound GDP with GTP. It contains a Sec7 domain, which may be responsible for guanine-nucleotide exchange activity and also brefeldin A inhibition. [provided by RefSeq, Aug 2011]
    Expression
    Ubiquitous expression in testis (RPKM 17.7), thyroid (RPKM 13.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARFGEF1 in Genome Data Viewer
    Location:
    8q13.2
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (67173511..67343781, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (67599967..67770273, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (68085746..68256016, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr8:68012735-68012945 Neighboring gene RNA, 5S ribosomal pseudogene 268 Neighboring gene centrosome and spindle pole associated protein 1 Neighboring gene uncharacterized LOC124901956 Neighboring gene nucleophosmin 1 pseudogene 44 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:68153855-68154652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68221915-68222570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68222571-68223225 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:68255030-68255710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19262 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:68261316-68261816 Neighboring gene ARFGEF1 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 12286 Neighboring gene CRISPRi-validated cis-regulatory element chr8.1934 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68280925-68281630 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:68281631-68282336 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:68293145-68293756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27499 Neighboring gene ribosomal protein L17 pseudogene 31 Neighboring gene carboxypeptidase A6 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:68424545-68425147 Neighboring gene uncharacterized LOC105375886 Neighboring gene NACA pseudogene 10

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The miR-133b/brefeldin A-inhibited guanine nucleotide-exchange protein 1 (ARFGEF1) axis represses proliferation, invasion, and migration in cervical cancer cells.
      Title: The miR-133b/brefeldin A-inhibited guanine nucleotide-exchange protein 1 (ARFGEF1) axis represses proliferation, invasion, and migration in cervical cancer cells.
    2. Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity.
      Title: Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity.
    3. BIG1 controls macrophage pro-inflammatory responses through ARF3-mediated PI(4,5)P2 synthesis.
      Title: BIG1 controls macrophage pro-inflammatory responses through ARF3-mediated PI(4,5)P2 synthesis.
    4. BIG1 and BIG2 knockdown significantly decreased the levels of VEGF mRNA and protein in glioblastoma U251 cells and HUVECs. Furthermore, depletion of BIG1 and BIG2 inhibited HUVEC angiogenesis by diminishing cell migration.
      Title: Involvement of BIG1 and BIG2 in regulating VEGF expression and angiogenesis.
    5. The findings provide structural insight into how Arf1 GEFs, and hence active Arf1, achieve their correct subcellular distribution.
      Title: Structural Insights into Arl1-Mediated Targeting of the Arf-GEF BIG1 to the trans-Golgi.
    6. The data demonstrate a novel and unexpected function of BIG1 that regulates TNFR1 signaling by targeting TRAF2.
      Title: Brefeldin A-Inhibited Guanine Nucleotide-Exchange Factor 1 (BIG1) Governs the Recruitment of Tumor Necrosis Factor Receptor-Associated Factor 2 (TRAF2) to Tumor Necrosis Factor Receptor 1 (TNFR1) Signaling Complexes.
    7. Both phospholipase D activity and vesicular trafficking were required for effects of BIG1 and BIG2 on beta-catenin activation. Levels of PKA-phosphorylated beta-catenin S675 and beta-catenin association with PKA, BIG1, and BIG2 were also diminished after BIG1/BIG2 depletion.
      Title: Enhancement of β-catenin activity by BIG1 plus BIG2 via Arf activation and cAMP signals.
    8. Arf guanine nucleotide-exchange factors BIG1 and BIG2 regulate nonmuscle myosin IIA activity by anchoring myosin phosphatase complex.
      Title: Arf guanine nucleotide-exchange factors BIG1 and BIG2 regulate nonmuscle myosin IIA activity by anchoring myosin phosphatase complex.
    9. an early acting GEF (GBF1) activates ARFs that mediate recruitment of late acting GEFs (BIG1/2) to coordinate coating events within the pre-Golgi/Golgi/TGN continuum.
      Title: The Sec7 guanine nucleotide exchange factor GBF1 regulates membrane recruitment of BIG1 and BIG2 guanine nucleotide exchange factors to the trans-Golgi network (TGN).
    10. BIG1, through its ability to activate ADP-ribosylation factor 1, regulates cell-surface levels and function of ABCA1.
      Title: BIG1, a brefeldin A-inhibited guanine nucleotide-exchange protein modulates ATP-binding cassette transporter A-1 trafficking and function.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Developmental delay, impaired speech, and behavioral abnormalities, with or without seizures
    MedGen: C5575272 OMIM: 619964 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Salt-inducible kinase 3, SIK3, is a new gene associated with hearing.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with ADP-ribosylation factor guanine nucleotide-exchange factor 1 (ARFGEF1; BIG1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZP434L057

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables myosin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase A regulatory subunit binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endomembrane system organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in exocytosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of actin filament polymerization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of wound healing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_positive_effect protein glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of ARF protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of establishment of cell polarity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of small nuclear ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    brefeldin A-inhibited guanine nucleotide-exchange protein 1
    Names
    ADP ribosylation factor guanine nucleotide exchange factor 1
    ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)
    p200 ARF guanine nucleotide exchange factor

    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_001413184.1 → NP_001400113.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359
      UniProtKB/Swiss-Prot
      Q9NV46, Q9UFV2, Q9UNL0, Q9Y6D6

    2. NM_001413185.1 → NP_001400114.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    3. NM_001413186.1 → NP_001400115.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    4. NM_001413187.1 → NP_001400116.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    5. NM_001413188.1 → NP_001400117.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    6. NM_001413189.1 → NP_001400118.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    7. NM_001413190.1 → NP_001400119.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    8. NM_001413191.1 → NP_001400120.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    9. NM_001413192.1 → NP_001400121.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    10. NM_001413193.1 → NP_001400122.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    11. NM_001413194.1 → NP_001400123.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    12. NM_001413195.1 → NP_001400124.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 11

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    13. NM_001413196.1 → NP_001400125.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 12

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359
      Related
      ENSP00000428429.2, ENST00000520381.5

    14. NM_001413197.1 → NP_001400126.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    15. NM_006421.5 → NP_006412.2  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform 1

      See identical proteins and their annotated locations for NP_006412.2

      Status: REVIEWED

      Source sequence(s)
      AC021321, AF111162, AI692863, AL117446, CA314908
      Consensus CDS
      CCDS6199.1
      UniProtKB/Swiss-Prot
      Q9NV46, Q9UFV2, Q9UNL0, Q9Y6D6
      Related
      ENSP00000262215.3, ENST00000262215.8
      Conserved Domains (5) summary
      PLN03076
      Location:15 → 1766
      PLN03076; ARF guanine nucleotide exchange factor (ARF-GEF); Provisional
      pfam01369
      Location:698 → 882
      Sec7; Sec7 domain
      pfam09324
      Location:1220 → 1301
      DUF1981; Domain of unknown function (DUF1981)
      pfam12783
      Location:419 → 573
      Sec7_N; Guanine nucleotide exchange factor in Golgi transport N-terminal
      pfam16213
      Location:29 → 210
      DCB; Dimerization and cyclophilin-binding domain of Mon2

    RNA

    1. NR_182117.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC021321, AC087359

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      67173511..67343781 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047421266.1 → XP_047277222.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      67599967..67770273 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359587.1 → XP_054215562.1  brefeldin A-inhibited guanine nucleotide-exchange protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6D6.2 GenPept UniProtKB/Swiss-Prot:Q9Y6D6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools