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    ARHGEF38 Rho guanine nucleotide exchange factor 38 [ Homo sapiens (human) ]

    Gene ID: 54848, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ARHGEF38provided by HGNC
    Official Full Name
    Rho guanine nucleotide exchange factor 38provided by HGNC
    Primary source
    HGNC:HGNC:25968
    See related
    Ensembl:ENSG00000236699 MIM:619919; AllianceGenome:HGNC:25968
    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
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in prostate (RPKM 3.4), colon (RPKM 1.7) and 11 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARHGEF38 in Genome Data Viewer
    Location:
    4q24
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (105552620..105682566)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (108863418..108993730)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (106473777..106602071)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377352 Neighboring gene ATP synthase F1 subunit epsilon pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:106476385-106476934 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:106477486-106478035 Neighboring gene ARHGEF38 intronic transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21783 Neighboring gene integrator complex subunit 12 Neighboring gene uncharacterized LOC124900748 Neighboring gene uncharacterized LOC124900747

    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. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes. Lansdon LA, et al. Am J Hum Genet, 2023 Jan 5. PMID 36493769, Free PMC Article
    2. Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. Hancock DB, et al. Nat Genet, 2010 Jan. PMID 20010835, Free PMC Article
    3. Gene network analysis in a pediatric cohort identifies novel lung function genes. Ong BA, et al. PLoS One, 2013. PMID 24023788, Free PMC Article
    4. Mutation of ARHGAP9 in patients with coronary spastic angina. Takefuji M, et al. J Hum Genet, 2010 Jan. PMID 19911011
    5. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. Kalsi G, et al. Hum Mol Genet, 2010 Jun 15. PMID 20332099, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes.
      Title: Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.
    4. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
    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
    Gene network analysis in a pediatric cohort identifies novel lung function genes.
    EBI GWAS Catalog
    Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function.
    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

    Clone Names

    • FLJ20184, FLJ43963

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    rho guanine nucleotide exchange factor 38
    Names
    Rho guanine nucleotide exchange factor (GEF) 38

    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_001242729.2 → NP_001229658.1  rho guanine nucleotide exchange factor 38 isoform 1

      See identical proteins and their annotated locations for NP_001229658.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC105391, AK000191, AK125951, DT932593
      Consensus CDS
      CCDS56338.1
      UniProtKB/Swiss-Prot
      C9JIB4, Q9NXL2
      Related
      ENSP00000416125.2, ENST00000420470.3
      Conserved Domains (4) summary
      cd07589
      Location:336 → 522
      BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein
      cd12141
      Location:717 → 773
      SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains
      pfam00621
      Location:98 → 284
      RhoGEF; RhoGEF domain
      cl17036
      Location:586 → 642
      SH3; Src Homology 3 domain superfamily

    2. NM_017700.2 → NP_060170.1  rho guanine nucleotide exchange factor 38 isoform 2

      See identical proteins and their annotated locations for NP_060170.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents an alternate 3' splice pattern with a shorter coding region, compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK000191
      Consensus CDS
      CCDS3670.1
      UniProtKB/Swiss-Prot
      Q9NXL2
      Related
      ENSP00000265154.2, ENST00000265154.6
      Conserved Domains (1) summary
      cl02571
      Location:98 → 194
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      105552620..105682566
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011532050.3 → XP_011530352.1  rho guanine nucleotide exchange factor 38 isoform X1

      Conserved Domains (4) summary
      cd07589
      Location:171 → 357
      BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein
      cd12141
      Location:552 → 608
      SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains
      cl02571
      Location:4 → 119
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
      cl17036
      Location:421 → 477
      SH3; Src Homology 3 domain superfamily

    2. XM_011532051.3 → XP_011530353.1  rho guanine nucleotide exchange factor 38 isoform X3

      Conserved Domains (2) summary
      pfam00621
      Location:98 → 284
      RhoGEF; RhoGEF domain
      cl12013
      Location:336 → 419
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    3. XM_006714244.4 → XP_006714307.1  rho guanine nucleotide exchange factor 38 isoform X2

      Conserved Domains (4) summary
      cd07589
      Location:118 → 304
      BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein
      cd12141
      Location:499 → 555
      SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains
      cl02571
      Location:1 → 66
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
      cl17036
      Location:368 → 424
      SH3; Src Homology 3 domain superfamily

    RNA

    1. XR_938749.4 RNA Sequence

    2. XR_007057934.1 RNA Sequence

    3. XR_938750.4 RNA Sequence

    4. XR_001741247.3 RNA Sequence

    5. XR_938751.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      108863418..108993730
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350283.1 → XP_054206258.1  rho guanine nucleotide exchange factor 38 isoform X1

    2. XM_054350285.1 → XP_054206260.1  rho guanine nucleotide exchange factor 38 isoform X3

    3. XM_054350284.1 → XP_054206259.1  rho guanine nucleotide exchange factor 38 isoform X2

    RNA

    1. XR_008486996.1 RNA Sequence

    2. XR_008486998.1 RNA Sequence

    3. XR_008486999.1 RNA Sequence

    4. XR_008486997.1 RNA Sequence

    5. XR_008487000.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NXL2.2 GenPept UniProtKB/Swiss-Prot:Q9NXL2

    Gene LinkOut

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

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