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    RGPD3 RANBP2 like and GRIP domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 653489, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RGPD3provided by HGNC
    Official Full Name
    RANBP2 like and GRIP domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:32416
    See related
    Ensembl:ENSG00000153165 MIM:612706; AllianceGenome:HGNC:32416
    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
    RGP3
    Summary
    This gene is located in a cluster of Ran-binding protein related genes on chromosome 2 which arose through duplication in primates. The encoded protein contains an N-terminal TPR (tetratricopeptide repeat) domain, two Ran-binding domains, and a C-terminal GRIP domain (golgin-97, RanBP2alpha, Imh1p and p230/golgin-245) domain. [provided by RefSeq, Sep 2011]
    Expression
    Broad expression in testis (RPKM 22.2), thyroid (RPKM 6.7) and 25 other tissues See more
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    Genomic context

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    See RGPD3 in Genome Data Viewer
    Location:
    2q12.2
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (106403406..106470935, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (106864167..106932361, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (107019862..107084869, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ANAPC1 pseudogene 6 Neighboring gene plasminogen like A (pseudogene) Neighboring gene ReSE screen-validated silencer GRCh37_chr2:107056244-107056460 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:107060799-107061300 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:107084140-107084332 Neighboring gene anaphase-promoting complex subunit 1-like Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:107118971-107119470 Neighboring gene CD8B family member 2 Neighboring gene uncharacterized LOC124907863

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Complex genomic rearrangements lead to novel primate gene function. Ciccarelli FD, et al. Genome Res, 2005 Mar. PMID 15710750, Free PMC Article
    2. Targeting SKA3 suppresses the proliferation and chemoresistance of laryngeal squamous cell carcinoma via impairing PLK1-AKT axis-mediated glycolysis. Gao W, et al. Cell Death Dis, 2020 Oct 26. PMID 33106477, Free PMC Article
    3. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? Nathan JA, et al. EMBO J, 2013 Feb 20. PMID 23314748, Free PMC Article
    4. Proximity labeling of endogenous RICTOR identifies mTOR complex 2 regulation by ADP ribosylation factor ARF1. Luciano AK, et al. J Biol Chem, 2022 Oct. PMID 35973513, Free PMC Article
    5. O-GlcNAcylation of SPOP promotes carcinogenesis in hepatocellular carcinoma. Zhou P, et al. Oncogene, 2023 Mar. PMID 36604567

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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)

    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
    contributes_to GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in NLS-bearing protein import into nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of nuclear pore IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ranBP2-like and GRIP domain-containing protein 3

    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_021160.1 RefSeqGene

      Range
      4933..69940
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001144013.2 → NP_001137485.1  ranBP2-like and GRIP domain-containing protein 3

      See identical proteins and their annotated locations for NP_001137485.1

      Status: REVIEWED

      Source sequence(s)
      AC097527, AC114755
      Consensus CDS
      CCDS46379.1
      UniProtKB/Swiss-Prot
      A6NKT7, B8ZZM4
      UniProtKB/TrEMBL
      J3KNE0
      Related
      ENSP00000386588.4, ENST00000409886.4
      Conserved Domains (8) summary
      COG5171
      Location:976 → 1168
      YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
      cd13177
      Location:1052 → 1168
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1349 → 1465
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      sd00006
      Location:59 → 89
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:60 → 92
      TPR_1; Tetratricopeptide repeat
      pfam01465
      Location:1708 → 1750
      GRIP; GRIP domain
      pfam13414
      Location:59 → 126
      TPR_11; TPR repeat
      pfam16704
      Location:1642 → 1706
      Rab_bind; Rab binding 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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      106403406..106470935 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004738.2 → XP_016860227.1  ranBP2-like and GRIP domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      J3KNE0
      Conserved Domains (6) summary
      smart00028
      Location:68 → 100
      TPR; Tetratricopeptide repeats
      smart00755
      Location:1716 → 1761
      Grip; golgin-97, RanBP2alpha,Imh1p and p230/golgin-245
      cd13177
      Location:1060 → 1176
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1357 → 1473
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      sd00006
      Location:68 → 96
      TPR; TPR repeat [structural motif]
      pfam16704
      Location:1650 → 1714
      Rab_bind; Rab binding domain

    2. XM_017004739.3 → XP_016860228.1  ranBP2-like and GRIP domain-containing protein 3 isoform X3

      UniProtKB/TrEMBL
      J3KNE0

    3. XM_047445567.1 → XP_047301523.1  ranBP2-like and GRIP domain-containing protein 3 isoform X2

      UniProtKB/TrEMBL
      J3KNE0

    4. XM_017004740.3 → XP_016860229.1  ranBP2-like and GRIP domain-containing protein 3 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      106864167..106932361 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343488.1 → XP_054199463.1  ranBP2-like and GRIP domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      J3KNE0

    2. XM_054343490.1 → XP_054199465.1  ranBP2-like and GRIP domain-containing protein 3 isoform X3

      UniProtKB/TrEMBL
      J3KNE0

    3. XM_054343489.1 → XP_054199464.1  ranBP2-like and GRIP domain-containing protein 3 isoform X2

      UniProtKB/TrEMBL
      J3KNE0

    4. XM_054343491.1 → XP_054199466.1  ranBP2-like and GRIP domain-containing protein 3 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NKT7.2 GenPept UniProtKB/Swiss-Prot:A6NKT7

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