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

    Gene ID: 285190, updated on 10-Dec-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, Dec 2024]
    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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    See RGPD4 in Genome Data Viewer
    Location:
    2q12.3
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (107826892..107892544)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (108288412..108354099)
    RS_2024_09 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: 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. 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. 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

    See all (19) 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

    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_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
      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

      UniProtKB/TrEMBL
      J3KNE0

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

      UniProtKB/TrEMBL
      J3KNE0

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

      UniProtKB/TrEMBL
      J3KNE0

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

      UniProtKB/TrEMBL
      J3KNE0

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

      UniProtKB/TrEMBL
      J3KNE0

    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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