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RGPD4 RANBP2 like and GRIP domain containing 4 [ Homo sapiens (human) ]

Gene ID: 285190, updated on 3-Apr-2024

Summary

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Official Symbol
RGPD4provided by HGNC
Official Full Name
RANBP2 like and GRIP domain containing 4provided by HGNC
Primary source
HGNC:HGNC:32417
See related
Ensembl:ENSG00000196862 MIM:612707; AllianceGenome:HGNC:32417
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
Also known as
RGP4
Summary
Predicted to contribute to GTPase activator activity. Predicted to be involved in NLS-bearing protein import into nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 18.2), thyroid (RPKM 5.7) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
2q12.3
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (107826892..107892544)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (108288412..108354099)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (108443348..108509000)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene gastric cancer associated transcript 1 Neighboring gene Sharpr-MPRA regulatory region 10849 Neighboring gene RGPD4 antisense RNA 1 (head to head) Neighboring gene uncharacterized LOC124906057 Neighboring gene ribosomal protein L22 pseudogene 8 Neighboring gene SRSF3 pseudogene 5

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. Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. Svendsen JM, et al. Cell, 2009 Jul 10. PMID 19596235, Free PMC Article
  3. Regulation of epidermal differentiation through KDF1-mediated deubiquitination of IKKα. Li Y, et al. EMBO Rep, 2020 May 6. PMID 32239614, Free PMC Article
  4. RSPO-LGR4 functions via IQGAP1 to potentiate Wnt signaling. Carmon KS, et al. Proc Natl Acad Sci U S A, 2014 Apr 1. PMID 24639526, Free PMC Article
  5. Proteome-wide analysis of USP14 substrates revealed its role in hepatosteatosis via stabilization of FASN. Liu B, et al. Nat Commun, 2018 Nov 13. PMID 30425250, Free PMC Article

See all (14) 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

Clone Names

  • DKFZp686P0288

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 4

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_182588.3 → NP_872394.2  ranBP2-like and GRIP domain-containing protein 4

    See identical proteins and their annotated locations for NP_872394.2

    Status: VALIDATED

    Source sequence(s)
    AC009963, AC096655
    Consensus CDS
    CCDS46381.1
    UniProtKB/Swiss-Prot
    B9A029, Q7Z3J3
    UniProtKB/TrEMBL
    J3KNE0
    Related
    ENSP00000386810.4, ENST00000408999.4
    Conserved Domains (8) summary
    smart00028
    Location:60 → 92
    TPR; Tetratricopeptide repeats
    COG5171
    Location:976 → 1169
    YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
    cd13177
    Location:1053 → 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]
    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
    107826892..107892544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511017.4 → XP_011509319.1  ranBP2-like and GRIP domain-containing protein 4 isoform X1

    UniProtKB/TrEMBL
    J3KNE0
    Conserved Domains (7) summary
    smart00028
    Location:60 → 92
    TPR; Tetratricopeptide repeats
    COG5171
    Location:976 → 1169
    YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
    cd13177
    Location:1053 → 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]
    pfam13414
    Location:59 → 126
    TPR_11; TPR repeat
    pfam16704
    Location:1642 → 1689
    Rab_bind; Rab binding domain

  2. XM_011511020.4 → XP_011509322.1  ranBP2-like and GRIP domain-containing protein 4 isoform X4

    UniProtKB/TrEMBL
    J3KNE0
    Conserved Domains (6) summary
    COG5171
    Location:976 → 1169
    YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
    cd13177
    Location:1053 → 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
    pfam13414
    Location:59 → 126
    TPR_11; TPR repeat

  3. XM_011511018.4 → XP_011509320.1  ranBP2-like and GRIP domain-containing protein 4 isoform X2

    UniProtKB/TrEMBL
    J3KNE0
    Conserved Domains (6) summary
    smart00028
    Location:60 → 92
    TPR; Tetratricopeptide repeats
    COG5171
    Location:976 → 1169
    YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
    cd13177
    Location:1053 → 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]
    pfam13414
    Location:59 → 126
    TPR_11; TPR repeat

  4. XM_011511019.4 → XP_011509321.1  ranBP2-like and GRIP domain-containing protein 4 isoform X3

    UniProtKB/TrEMBL
    J3KNE0
    Conserved Domains (6) summary
    COG5171
    Location:976 → 1169
    YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
    cd13177
    Location:1053 → 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
    pfam13414
    Location:59 → 126
    TPR_11; TPR repeat

  5. XM_017003898.2 → XP_016859387.1  ranBP2-like and GRIP domain-containing protein 4 isoform X5

RNA

  1. XR_922911.4 RNA Sequence

  2. XR_007073111.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    108288412..108354099
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341523.1 → XP_054197498.1  ranBP2-like and GRIP domain-containing protein 4 isoform X1

  2. XM_054341527.1 → XP_054197502.1  ranBP2-like and GRIP domain-containing protein 4 isoform X4

  3. XM_054341525.1 → XP_054197500.1  ranBP2-like and GRIP domain-containing protein 4 isoform X7

  4. XM_054341526.1 → XP_054197501.1  ranBP2-like and GRIP domain-containing protein 4 isoform X3

  5. XM_054341524.1 → XP_054197499.1  ranBP2-like and GRIP domain-containing protein 4 isoform X6

  6. XM_054341528.1 → XP_054197503.1  ranBP2-like and GRIP domain-containing protein 4 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z3J3.3 GenPept UniProtKB/Swiss-Prot:Q7Z3J3

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