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    RAB40A RAB40A, member RAS oncogene family [ Homo sapiens (human) ]

    Gene ID: 142684, updated on 2-Nov-2024

    Summary

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    Official Symbol
    RAB40Aprovided by HGNC
    Official Full Name
    RAB40A, member RAS oncogene familyprovided by HGNC
    Primary source
    HGNC:HGNC:18283
    See related
    Ensembl:ENSG00000172476 MIM:301065; AllianceGenome:HGNC:18283
    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
    RAR2; RAR2A
    Summary
    This gene encodes a member of the Rab40 subfamily of Rab small GTP-binding proteins that contains a C-terminal suppressors of cytokine signaling box. [provided by RefSeq, Apr 2010]
    Expression
    Broad expression in esophagus (RPKM 1.8), testis (RPKM 1.2) and 15 other tissues See more
    Orthologs
    all
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    Genomic context

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    See RAB40A in Genome Data Viewer
    Location:
    Xq22.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (103493266..103519489, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (101946141..101966502, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (102754058..102774417, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905204 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:102610887-102612086 Neighboring gene transcription elongation factor A like 9 Neighboring gene uncharacterized LL0XNC01-250H12.3 Neighboring gene brain expressed X-linked 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29817 Neighboring gene MPRA-validated peak7415 silencer Neighboring gene NANOG hESC enhancer GRCh37_chrX:102679147-102679648 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:102689981-102690482 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:102690483-102690982 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:102695365-102696050 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:102696051-102696737 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:102715105-102715604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29820 Neighboring gene long intergenic non-protein coding RNA 2589 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:102809676-102810875 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:102840363-102841076 Neighboring gene transcription elongation factor A like 4

    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. Rab40C is a novel Varp-binding protein that promotes proteasomal degradation of Varp in melanocytes. Yatsu A, et al. Biol Open, 2015 Feb 6. PMID 25661869, Free PMC Article
    2. Regulation of lipid homeostasis by the TBC protein dTBC1D22 via modulation of the small GTPase Rab40 to facilitate lipophagy. Duan X, et al. Cell Rep, 2021 Aug 31. PMID 34469730
    3. Pericentrosomal targeting of Rab6 secretory vesicles by Bicaudal-D-related protein 1 (BICDR-1) regulates neuritogenesis. Schlager MA, et al. EMBO J, 2010 May 19. PMID 20360680, Free PMC Article
    4. Evolution of the Rab family of small GTP-binding proteins. Pereira-Leal JB, et al. J Mol Biol, 2001 Nov 2. PMID 11697911
    5. Genome-wide shRNA screening identifies host factors involved in early endocytic events for HIV-1-induced CD4 down-regulation. Landi A, et al. Retrovirology, 2014 Dec 13. PMID 25496667, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Genome-wide shRNA screening identifies RAB40A, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC142061

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    colocalizes_with Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with lipid droplet IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in synaptic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ras-related protein Rab-40A
    Names
    SOCS box-containing protein RAR2A
    protein Rar-2

    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.

    Genomic

    1. NG_017149.1 RefSeqGene

      Range
      5001..25360
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_080879.3 → NP_543155.2  ras-related protein Rab-40A

      See identical proteins and their annotated locations for NP_543155.2

      Status: REVIEWED

      Source sequence(s)
      AF132748, AF422143, H24206, Z69733
      Consensus CDS
      CCDS35357.1
      UniProtKB/Swiss-Prot
      O00407, Q17RQ5, Q6DK06, Q8TF06, Q8WXH6
      Related
      ENSP00000305648.1, ENST00000304236.2
      Conserved Domains (2) summary
      cd03742
      Location:187 → 228
      SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...
      cl21455
      Location:9 → 277
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      103493266..103519489 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441843.1 → XP_047297799.1  ras-related protein Rab-40A isoform X1

      UniProtKB/Swiss-Prot
      O00407, Q17RQ5, Q6DK06, Q8TF06, Q8WXH6

    2. XM_047441844.1 → XP_047297800.1  ras-related protein Rab-40A isoform X1

      UniProtKB/Swiss-Prot
      O00407, Q17RQ5, Q6DK06, Q8TF06, Q8WXH6
      Related
      ENSP00000361716.1, ENST00000372633.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      101946141..101966502 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WXH6.2 GenPept UniProtKB/Swiss-Prot:Q8WXH6

    Gene LinkOut

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

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