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

Gene ID: 653489, updated on 3-Apr-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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Location:
2q12.2
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (106403406..106470935, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (106864167..106932361, complement)
105.20220307 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: 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. 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. Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression. Diner BA, et al. Mol Cell Proteomics, 2015 Sep. PMID 25693804, Free PMC Article
  5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Hillier LW, et al. Nature, 2005 Apr 7. PMID 15815621

See all (25) 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)

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
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_2023_10

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

  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

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

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

  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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