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

Gene ID: 84220, updated on 3-Apr-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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Location:
2q13
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (109760618..109857705)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (110221679..110319403)
105.20220307 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: 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. 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 (23) 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

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
  
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_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
    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

  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

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

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

Gene LinkOut

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