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

    Gene ID: 400966, updated on 10-Dec-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, Dec 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86913659..87013976)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86915628..87019191)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (87140782..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: 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. 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. 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
    5. 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

    See all (28) 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)

    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
      B4DYH0, F8VYC4
      Related
      ENSP00000381253.3, ENST00000398193.8

    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
      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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0

    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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0

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

      UniProtKB/TrEMBL
      B4DYH0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0DJD0.1 GenPept UniProtKB/Swiss-Prot:P0DJD0

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