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    RGPD5 RANBP2 like and GRIP domain containing 5 [ Homo sapiens (human) ]

    Gene ID: 84220, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RGPD5provided by HGNC
    Official Full Name
    RANBP2 like and GRIP domain containing 5provided by HGNC
    Primary source
    HGNC:HGNC:32418
    See related
    Ensembl:ENSG00000015568 MIM:612708; AllianceGenome:HGNC:32418
    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
    BS63; RGP5; BS-63; HEL161
    Summary
    RAN is a small GTP-binding protein of the RAS superfamily that is associated with the nuclear membrane and is thought to control a variety of cellular functions through its interactions with other proteins. This gene shares a high degree of sequence identity with RANBP2, a large RAN-binding protein localized at the cytoplasmic side of the nuclear pore complex. It is believed that this RANBP2 gene family member arose from a duplication event 3 Mb distal to RANBP2. Alternative splicing has been observed for this locus and two variants are described. Additional splicing is suggested but complete sequence for further transcripts has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 33.7), brain (RPKM 11.6) and 25 other tissues See more
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    Genomic context

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    See RGPD5 in Genome Data Viewer
    Location:
    2q13
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (109760618..109857705)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (110221679..110319403)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (110550335..110615282)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RAN binding protein 2 Neighboring gene uncharacterized LOC100506563 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:110546857-110547358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:110549157-110549656 Neighboring gene ribosomal protein L22 pseudogene 11 Neighboring gene SRSF3 pseudogene 6 Neighboring gene LIMS3-LOC440895 readthrough Neighboring gene uncharacterized LOC102724848 Neighboring gene 2q13 recombination region Neighboring gene uncharacterized LOC105373547 Neighboring gene LIM zinc finger domain containing 3

    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. Molecular cloning and characterization of a novel testis-specific nucleoporin-related gene. Wang LF, et al. Arch Androl, 1999 Mar-Apr. PMID 10101573
    2. [Determination of the binding site of testis-specific nucleoporin BS-63 to transportin (karopherin beta 2) and the proof of their combination in vitro]. Cai Y, et al. Zhongguo Yi Xue Ke Xue Yuan Xue Bao, 2001 Oct. PMID 12905863
    3. Identification of a novel Ran binding protein 2 related gene (RANBP2L1) and detection of a gene cluster on human chromosome 2q11-q12. Nothwang HG, et al. Genomics, 1998 Feb 1. PMID 9480752
    4. Characterization and potential function of a novel testis-specific nucleoporin BS-63. Cai Y, et al. Mol Reprod Dev, 2002 Jan. PMID 11774384
    5. Complex genomic rearrangements lead to novel primate gene function. Ciccarelli FD, et al. Genome Res, 2005 Mar. PMID 15710750, Free PMC Article

    See all (30) 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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of RANBP2-like and GRIP domain containing 5 (RGPD5) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl 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

    • DKFZp686I1842

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 5/6
    Names
    RANBP2-like and GRIP domain-containing protein 5
    epididymis luminal protein 161
    ran-binding protein 2-like 1
    ran-binding protein 2-like 1/2
    ranBP2-like 1
    ranBP2-like 1/2
    ranBP2L1
    sperm membrane protein BS-63

    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_005054.3 → NP_005045.2  RANBP2-like and GRIP domain-containing protein 5/6 isoform 1

      See identical proteins and their annotated locations for NP_005045.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the longest transcript encoding the largest isoform (1).
      Source sequence(s)
      AC013271, AL044843, AL136868, BU631831, CA446006, U64675
      Consensus CDS
      CCDS2082.1
      UniProtKB/Swiss-Prot
      Q53QN2, Q53T03, Q59GM7, Q99666, Q9H0B2
      UniProtKB/TrEMBL
      A0A8Q3SIN4, V9HWE4
      Related
      ENSP00000016946.3, ENST00000016946.8
      Conserved Domains (8) summary
      COG5171
      Location:975 → 1167
      YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
      cd13177
      Location:1051 → 1167
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1348 → 1464
      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:1707 → 1749
      GRIP; GRIP domain
      pfam13414
      Location:59 → 126
      TPR_11; TPR repeat
      pfam16704
      Location:1641 → 1705
      Rab_bind; Rab binding domain

    2. NM_032260.3 → NP_115636.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform 2

      See identical proteins and their annotated locations for NP_115636.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate 3' terminal exon and is truncated, compared to variant 1. The encoded isoform (2) is shorter than isoform 1 and has a unique C-terminus.
      Source sequence(s)
      AC013271
      Consensus CDS
      CCDS2083.1
      Related
      ENSP00000376962.1, ENST00000393283.5
      Conserved Domains (3) summary
      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

    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
      109760618..109857705
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006712794.5 → XP_006712857.2  RANBP2-like and GRIP domain-containing protein 5/6 isoform X1

      UniProtKB/TrEMBL
      A0A8Q3SIN4
      Conserved Domains (8) summary
      COG5171
      Location:1001 → 1193
      YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
      cd13177
      Location:1077 → 1193
      RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
      cd14685
      Location:1374 → 1490
      RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
      sd00006
      Location:85 → 115
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:86 → 118
      TPR_1; Tetratricopeptide repeat
      pfam01465
      Location:1733 → 1775
      GRIP; GRIP domain
      pfam13414
      Location:85 → 152
      TPR_11; TPR repeat
      pfam16704
      Location:1667 → 1731
      Rab_bind; Rab binding domain

    2. XM_047445980.1 → XP_047301936.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X2

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    3. XM_017005081.3 → XP_016860570.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X3

      UniProtKB/TrEMBL
      A0A8Q3SIN4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      110221679..110319403
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344144.1 → XP_054200119.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X2

      UniProtKB/TrEMBL
      J3KNE0

    2. XM_054344145.1 → XP_054200120.1  RANBP2-like and GRIP domain-containing protein 5/6 isoform X3

      UniProtKB/TrEMBL
      J3KNE0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99666.3 GenPept UniProtKB/Swiss-Prot:Q99666

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