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    ARHGEF16 Rho guanine nucleotide exchange factor 16 [ Homo sapiens (human) ]

    Gene ID: 27237, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ARHGEF16provided by HGNC
    Official Full Name
    Rho guanine nucleotide exchange factor 16provided by HGNC
    Primary source
    HGNC:HGNC:15515
    See related
    Ensembl:ENSG00000130762 MIM:618871; AllianceGenome:HGNC:15515
    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
    NBR; GEF16
    Summary
    Although the specific function of this protein is not known yet, it is thought to be involved in protein-protein and protein-lipid interactions. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in duodenum (RPKM 15.0), small intestine (RPKM 12.9) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARHGEF16 in Genome Data Viewer
    Location:
    1p36.32
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3454665..3481113)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (2959327..2988135)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3371229..3397677)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene PR/SET domain 16 Neighboring gene collagen alpha-5(IV) chain-like Neighboring gene VISTA enhancer hs705 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3191818-3193017 Neighboring gene Sharpr-MPRA regulatory region 1987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3212462-3212962 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:3215870-3217069 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3220731-3221288 Neighboring gene uncharacterized LOC105378604 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3229262-3230461 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:3231799-3232358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3235695-3236196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3236197-3236696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3237397-3238015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3246879-3247556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3255514-3256329 Neighboring gene VISTA enhancer hs1912 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3268668-3269642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3269643-3270616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3272921-3273812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3273813-3274702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3277409-3277908 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:3285513-3286094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3303704-3304204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3304205-3304705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3307961-3308462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3311898-3312581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3312582-3313264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3320127-3320627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3325025-3325602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3332377-3333072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3331680-3332376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3337228-3337728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3350015-3350524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3357159-3357921 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3369311-3370063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3373825-3374576 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7120 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3388131-3388756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3399659-3400494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3400495-3401329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3408710-3409234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3408184-3408709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 119 Neighboring gene MEGF6 intron CAGE-defined mid-level expression enhancer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3439723-3440262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3445841-3446528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3447217-3447902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3449965-3450651 Neighboring gene multiple EGF like domains 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3459643-3460294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3460295-3460948 Neighboring gene MPRA-validated peak19 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3463961-3464599 Neighboring gene uncharacterized LOC105378608 Neighboring gene microRNA 551a

    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. Analogues of Y27632 increase gap junction communication and suppress the formation of transformed NIH3T3 colonies. Hampson L, et al. Br J Cancer, 2009 Sep 1. PMID 19707205, Free PMC Article
    2. Arhgef16, a novel Elmo1 binding partner, promotes clearance of apoptotic cells via RhoG-dependent Rac1 activation. Lee J, et al. Biochim Biophys Acta, 2014 Nov. PMID 25063526
    3. EphA2 phosphorylation at Ser897 by the Cdk1/MEK/ERK/RSK pathway regulates M-phase progression via maintenance of cortical rigidity. Kaibori Y, et al. FASEB J, 2019 Apr. PMID 30668924
    4. FYN is required for ARHGEF16 to promote proliferation and migration in colon cancer cells. Yu B, et al. Cell Death Dis, 2020 Aug 7. PMID 32811808, Free PMC Article
    5. GLI2 promotes cell proliferation and migration through transcriptional activation of ARHGEF16 in human glioma cells. Huang D, et al. J Exp Clin Cancer Res, 2018 Oct 11. PMID 30305138, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FYN is required for ARHGEF16 to promote proliferation and migration in colon cancer cells.
      Title: FYN is required for ARHGEF16 to promote proliferation and migration in colon cancer cells.
    2. Authors found that ARHGEF16 mRNA level was upregulated in U87 cells overexpressing GLI2A relative to control cells. GLI2 binds to the ARHGEF16 promoter and activates gene transcription. Glioma cells U87 and U118 overexpressing ARHGEF16 showed enhanced migration and proliferation.
      Title: GLI2 promotes cell proliferation and migration through transcriptional activation of ARHGEF16 in human glioma cells.
    3. Sixty-four novel structural analogues of Y27632 were synthesized and tested for their ability to persistently inhibit the transformation of NIH3T3 cells by Rho guanidine exchange factor 16 (ARHGEF16) or Ras.
      Title: Analogues of Y27632 increase gap junction communication and suppress the formation of transformed NIH3T3 colonies.
    4. These data suggest that HPV16 E6, Tip-1 and ARHGEF16 may cooperate to activate Cdc42 and support a potential link between the expression of HPV16 E6 and Cdc42 activation
      Title: The HPV16 E6 binding protein Tip-1 interacts with ARHGEF16, which activates Cdc42.
    5. The ephexin4 protein mediates cell migration through a RhoG-dependent mechanism.
      Title: Ephexin4 and EphA2 mediate cell migration through a RhoG-dependent mechanism.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Mutation of ARHGAP9 in patients with coronary spastic angina.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association of lipid-lowering response to statins in combined study populations.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables PDZ domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables cadherin binding HDA PubMed 
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables receptor tyrosine kinase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in activation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in activation of GTPase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein localization to plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    rho guanine nucleotide exchange factor 16
    Names
    Rho guanine exchange factor (GEF) 16
    Rho guanine nucleotide exchange factor (GEF) 16
    ephexin-4
    ephexin4

    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_014448.4 → NP_055263.2  rho guanine nucleotide exchange factor 16

      See identical proteins and their annotated locations for NP_055263.2

      Status: REVIEWED

      Source sequence(s)
      AL512413
      Consensus CDS
      CCDS46.2
      UniProtKB/Swiss-Prot
      Q5VV41, Q86TF0, Q99434
      UniProtKB/TrEMBL
      A0A2X0SFX5, B3KTS4
      Related
      ENSP00000367629.4, ENST00000378378.9
      Conserved Domains (4) summary
      cd11938
      Location:633 → 686
      SH3_ARHGEF16_26; Src homology 3 domain of the Rho guanine nucleotide exchange factors ARHGEF16 and ARHGEF26
      cd01221
      Location:489 → 622
      PH_ephexin; Ephexin Pleckstrin homology (PH) domain
      pfam00169
      Location:501 → 620
      PH; PH domain
      pfam00621
      Location:288 → 467
      RhoGEF; RhoGEF domain

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      3454665..3481113
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001051.2 → XP_016856540.1  rho guanine nucleotide exchange factor 16 isoform X2

      UniProtKB/Swiss-Prot
      Q5VV41, Q86TF0, Q99434
      UniProtKB/TrEMBL
      A0A2X0SFX5, B3KTS4
      Conserved Domains (4) summary
      cd11938
      Location:633 → 686
      SH3_ARHGEF16_26; Src homology 3 domain of the Rho guanine nucleotide exchange factors ARHGEF16 and ARHGEF26
      cd01221
      Location:489 → 622
      PH_ephexin; Ephexin Pleckstrin homology (PH) domain
      pfam00169
      Location:501 → 620
      PH; PH domain
      pfam00621
      Location:288 → 467
      RhoGEF; RhoGEF domain

    2. XM_017001049.2 → XP_016856538.1  rho guanine nucleotide exchange factor 16 isoform X1

      UniProtKB/TrEMBL
      A0A2X0SFX5

    3. XM_047418009.1 → XP_047273965.1  rho guanine nucleotide exchange factor 16 isoform X4

    4. XM_024446454.2 → XP_024302222.1  rho guanine nucleotide exchange factor 16 isoform X3

      UniProtKB/TrEMBL
      B4DJM7
      Related
      ENSP00000367624.1, ENST00000378373.5
      Conserved Domains (3) summary
      cd11938
      Location:345 → 398
      SH3_ARHGEF16_26; Src homology 3 domain of the Rho guanine nucleotide exchange factors ARHGEF16 and ARHGEF26
      cd01221
      Location:201 → 334
      PH_ephexin; Ephexin Pleckstrin homology (PH) domain
      pfam00621
      Location:1 → 178
      RhoGEF; RhoGEF domain

    5. XM_024446455.2 → XP_024302223.1  rho guanine nucleotide exchange factor 16 isoform X3

      UniProtKB/TrEMBL
      B4DJM7
      Related
      ENSP00000367622.2, ENST00000378371.6
      Conserved Domains (3) summary
      cd11938
      Location:345 → 398
      SH3_ARHGEF16_26; Src homology 3 domain of the Rho guanine nucleotide exchange factors ARHGEF16 and ARHGEF26
      cd01221
      Location:201 → 334
      PH_ephexin; Ephexin Pleckstrin homology (PH) domain
      pfam00621
      Location:1 → 178
      RhoGEF; RhoGEF domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      2959327..2988135
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336013.1 → XP_054191988.1  rho guanine nucleotide exchange factor 16 isoform X2

    2. XM_054336012.1 → XP_054191987.1  rho guanine nucleotide exchange factor 16 isoform X1

    3. XM_054336016.1 → XP_054191991.1  rho guanine nucleotide exchange factor 16 isoform X5

    4. XM_054336014.1 → XP_054191989.1  rho guanine nucleotide exchange factor 16 isoform X3

    5. XM_054336015.1 → XP_054191990.1  rho guanine nucleotide exchange factor 16 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VV41.1 GenPept UniProtKB/Swiss-Prot:Q5VV41

    Gene LinkOut

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

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