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RGPD1 RANBP2 like and GRIP domain containing 1 [ Homo sapiens (human) ]

Gene ID: 400966, updated on 3-Apr-2024

Summary

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Official Symbol
RGPD1provided by HGNC
Official Full Name
RANBP2 like and GRIP domain containing 1provided by HGNC
Primary source
HGNC:HGNC:32414
See related
Ensembl:ENSG00000187627 MIM:612704; AllianceGenome:HGNC:32414
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
RGP1; RGPD2; RanBP2L2; ranBP2L6
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 17.9), liver (RPKM 7.1) and 23 other tissues See more
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Genomic context

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See RGPD1 in Genome Data Viewer
Location:
2p11.2
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86913659..87013976)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86915628..87019191)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (87144738..87241099)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11721 Neighboring gene CD8 subunit alpha Neighboring gene MPRA-validated peak3783 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87066785-87067341 Neighboring gene CD8 subunit beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87083199-87083700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:87083701-87084200 Neighboring gene ANAPC1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:87169373-87170136 Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 pseudogene 5 Neighboring gene WBP1 pseudogene 1 Neighboring gene plasminogen like B1 Neighboring gene ANAPC1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11723 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11725 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:87303801-87304306 Neighboring gene tRNA-Pro (anticodon AGG) 4-1

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. Proteomic Analysis Reveals a Role for RSK in p120-catenin Phosphorylation and Melanoma Cell-Cell Adhesion. Méant A, et al. Mol Cell Proteomics, 2020 Jan. PMID 31678930, Free PMC Article
  3. Interactomes of Glycogen Synthase Kinase-3 Isoforms. Cormier KW, et al. J Proteome Res, 2023 Mar 3. PMID 36779422, Free PMC Article
  4. Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing. Freund EC, et al. Cell Rep, 2020 May 19. PMID 32433965, Free PMC Article
  5. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Jeronimo C, et al. Mol Cell, 2007 Jul 20. PMID 17643375, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Submit: New GeneRIF Correction

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

  • FLJ58076

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 1
Names
RANBP2-like and GRIP domain-containing protein 1/2
ran-binding protein 2-like 2/6
ran-binding protein 2-like 6
ranBP2-like 2/6
ranBP2-like 6

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_001024457.4 → NP_001019628.3  RANBP2-like and GRIP domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001019628.3

    Status: VALIDATED

    Source sequence(s)
    AC111200, CR749330
    UniProtKB/Swiss-Prot
    P0C839, P0DJD0, Q68DN6, Q6V1X0
    UniProtKB/TrEMBL
    B4DYH0
    Conserved Domains (8) summary
    smart00028
    Location:51 → 82
    TPR; Tetratricopeptide repeats
    COG5171
    Location:960 → 1152
    YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
    cd13177
    Location:1036 → 1152
    RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
    cd14685
    Location:1333 → 1449
    RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
    sd00006
    Location:50 → 80
    TPR; TPR repeat [structural motif]
    pfam01465
    Location:1690 → 1732
    GRIP; GRIP domain
    pfam13414
    Location:50 → 117
    TPR_11; TPR repeat
    pfam16704
    Location:1626 → 1686
    Rab_bind; Rab binding domain

  2. NM_001382344.1 → NP_001369273.1  RANBP2-like and GRIP domain-containing protein 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC111200
    Consensus CDS
    CCDS92800.1
    UniProtKB/TrEMBL
    A0A286YES2, B4DYH0
    Related
    ENSP00000492954.1, ENST00000641458.2
    Conserved Domains (7) summary
    smart00028
    Location:59 → 90
    TPR; Tetratricopeptide repeats
    COG0457
    Location:29 → 105
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    cd13177
    Location:1044 → 1160
    RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
    cd14685
    Location:1341 → 1457
    RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
    sd00006
    Location:58 → 88
    TPR; TPR repeat [structural motif]
    pfam16704
    Location:1634 → 1694
    Rab_bind; Rab binding domain
    pfam01465
    Location:1698 → 1740
    GRIP; GRIP domain

  3. NM_001410915.1 → NP_001397844.1  RANBP2-like and GRIP domain-containing protein 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC111200
    Consensus CDS
    CCDS92799.1
    UniProtKB/TrEMBL
    F8VYC4
    Related
    ENSP00000381253.3, ENST00000398193.8

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
    86913659..87013976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532845.4 → XP_011531147.1  RANBP2-like and GRIP domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    B4DYH0
    Conserved Domains (8) summary
    smart00028
    Location:104 → 135
    TPR; Tetratricopeptide repeats
    COG5171
    Location:1013 → 1205
    YRB1; Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
    cd13177
    Location:1089 → 1205
    RanBD2_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 2
    cd14685
    Location:1386 → 1502
    RanBD3_RanBP2-like; Ran-binding protein 2, Ran binding domain repeat 3
    sd00006
    Location:103 → 133
    TPR; TPR repeat [structural motif]
    pfam01465
    Location:1743 → 1785
    GRIP; GRIP domain
    pfam13414
    Location:103 → 170
    TPR_11; TPR repeat
    pfam16704
    Location:1679 → 1739
    Rab_bind; Rab binding domain

  2. XM_011532852.4 → XP_011531154.2  RANBP2-like and GRIP domain-containing protein 1 isoform X5

  3. XM_011532849.4 → XP_011531151.2  RANBP2-like and GRIP domain-containing protein 1 isoform X2

  4. XM_011532851.4 → XP_011531153.2  RANBP2-like and GRIP domain-containing protein 1 isoform X4

  5. XM_011532850.3 → XP_011531152.2  RANBP2-like and GRIP domain-containing protein 1 isoform X3

RNA

  1. XR_007074605.1 RNA Sequence

  2. XR_007074622.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    86915628..87019191
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342033.1 → XP_054198008.1  RANBP2-like and GRIP domain-containing protein 1 isoform X11

  2. XM_054342028.1 → XP_054198003.1  RANBP2-like and GRIP domain-containing protein 1 isoform X6

  3. XM_054342029.1 → XP_054198004.1  RANBP2-like and GRIP domain-containing protein 1 isoform X7

  4. XM_054342031.1 → XP_054198006.1  RANBP2-like and GRIP domain-containing protein 1 isoform X9

  5. XM_054342030.1 → XP_054198005.1  RANBP2-like and GRIP domain-containing protein 1 isoform X8

  6. XM_054342032.1 → XP_054198007.1  RANBP2-like and GRIP domain-containing protein 1 isoform X10

  7. XM_054342034.1 → XP_054198009.1  RANBP2-like and GRIP domain-containing protein 1 isoform X12

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0DJD0.1 GenPept UniProtKB/Swiss-Prot:P0DJD0

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