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RGPD3 Gene

protein-coding   GIFtS: 35
GCID: GC02M107007

RANBP2-Like And GRIP Domain Containing 3

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
RANBP2-Like And GRIP Domain Containing 31 2
RGP32 3 5
RanBP2-Like And GRIP Domain-Containing Protein 32

External Ids:    HGNC: 324161   Entrez Gene: 6534892   Ensembl: ENSG000001531657   OMIM: 6127065   UniProtKB: A6NKT73   

Export aliases for RGPD3 gene to outside databases

Previous GC identifers: GC00U921699 GC02U900831 GC02M106373


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RGPD3 Gene:
This gene is located in a cluster of Ran-binding protein related genes on chromosome 2 which arose through
duplication in primates. The encoded protein contains an N-terminal TPR (tetratricopeptide repeat) domain, two
Ran-binding domains, and a C-terminal GRIP domain (golgin-97, RanBP2alpha, Imh1p and p230/golgin-245) domain.
(provided by RefSeq, Sep 2011)

GeneCards Summary for RGPD3 Gene:
RGPD3 (RANBP2-like and GRIP domain containing 3) is a protein-coding gene. An important paralog of this gene is PPIE.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the RGPD3 gene promoter:
         Sp1   Nkx2-5   NF-AT   AREB6   NF-AT4   Pax-3   NF-AT2   NF-AT3   ZIC2/Zic2   NF-AT1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RGPD3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RGPD3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q13   Ensembl cytogenetic band:  2q12.2   HGNC cytogenetic band: 2q12.2

RGPD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RGPD3 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M107007:  view genomic region     (about GC identifiers)

Start:
107,021,136 bp from pter      End:
107,084,832 bp from pter
Size:
63,697 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: RGPD3_HUMAN, A6NKT7 (See protein sequence)
Recommended Name: RanBP2-like and GRIP domain-containing protein 3  
Size: 1758 amino acids; 197487 Da
Miscellaneous: One of the 8 copies of RANBP2 clustered close to the chromosome 2 centromere
Secondary accessions: B8ZZM4

Explore the universe of human proteins at neXtProt for RGPD3: NX_A6NKT7

Explore proteomics data for RGPD3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys106, Lys799, Lys1086, Lys1181, Lys1206, Lys1383, Lys1421, Lys1449
  • Modification sites at PhosphoSitePlus

  • See RGPD3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001137485.1  
    ENSEMBL proteins: 
     ENSP00000386588   ENSP00000303659  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    TTC: Tetratricopeptide (TTC) repeat domain containing

    Selected InterPro protein domains (see all 7):
     IPR000156 Ran_bind_dom
     IPR011990 TPR-like_helical
     IPR011993 PH_like_dom
     IPR001440 TPR_1
     IPR000237 GRIP

    Graphical View of Domain Structure for InterPro Entry A6NKT7

    ProtoNet protein and cluster: A6NKT7

    UniProtKB/Swiss-Prot: RGPD3_HUMAN, A6NKT7
    Similarity: Contains 1 GRIP domain
    Similarity: Contains 2 RanBD1 domains
    Similarity: Contains 2 TPR repeats


    Find genes that share domains with RGPD3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with RGPD3           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RGPD3

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    nucleus2
    cytoskeleton1
    mitochondrion1
    peroxisome1
    plasma membrane1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RGPD3
    Interactions:

        Search GeneGlobe Interaction Network for RGPD3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for RGPD3 (ENSP000003865884) via UniProtKB, MINT, STRING, and/or I2D (see all 34)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CARM1ENSP000003256904STRING: ENSP00000325690
    NXT2ENSP000002180044STRING: ENSP00000218004
    TMEM194AENSP000003001284STRING: ENSP00000300128
    UBCENSP000003448184STRING: ENSP00000344818
    NUP155ENSP000002314984STRING: ENSP00000231498
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000042protein targeting to Golgi IEA--
    GO:0046907intracellular transport ----

    Find genes that share ontologies with RGPD3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RGPD3



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for RGPD3 gene: 
    NM_001144013.1  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000409886(uc010ywi.1) ENST00000304514
    miRNA
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    hsa-miR-544b hsa-miR-27a hsa-miR-145 hsa-miR-27b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    RGPD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    RGPD3 Expression
    About this image


    RGPD3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Testis (Reproductive System)    fully expand to see all 3 entries
             Leydig Cells Testis Interstitium
             Testis Interstitium
    RGPD3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RGPD3 Protein Expression
        Custom PCR Arrays for RGPD3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RGPD3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for RGPD3 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ranbp21 RAN binding protein 2 87.97(n)
    88.42(a)
      19386  NM_011240.3  NP_035370.2 
    chicken
    (Gallus gallus)
    Aves RANBP21 RAN binding protein 2 71(n)
    68.89(a)
      418730  XM_416929.4  XP_416929.4 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    42(a)
    1 → many
    3(107454117-107504389)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ranbp21 RAN binding protein 2 66.56(n)
    62.52(a)
      100134999  XM_002937658.2  XP_002937704.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch1073-55a19.21 si:ch1073-55a19.2 56.38(n)
    54.65(a)
      100317326  XM_005169115.1  XP_005169172.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG50716
    --
    14(a)
    1 → many
    3R(21444136-21446401)
    worm
    (Caenorhabditis elegans)
    Secernentea T22F3.126
    Y17G9B.46
    Protein Y17G9B.4 (Y17G9B.4) mRNA, complete cds
    7(a)
    13(a)
    many ↔ many
    many ↔ many
    V(3589029-3592199) WBGene00044705
    IV(4752094-4753230) WBGene00021201


    ENSEMBL Gene Tree for RGPD3 (if available)
    TreeFam Gene Tree for RGPD3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RGPD3 gene
    RGPD41 2  RGPD11 2  RGPD81 2  RGPD51 2  RGPD61 2  RGPD21 2  PPIE2  PPIAL4C2  
    RANBP22  PPIF2  PPIA2  PPIAL4D2  PPIAL4A2  PPIAL4G2  PPIAL4B2  
    8 SIMAP similar genes for RGPD3 using alignment to 2 protein entries:     RGPD3_HUMAN (see all proteins):
    RGPD4    RGPD1    RGPD2    RGPD5    RGPD6    RGPD8
    RANBP1    RANBP2

    Find genes that share paralogs with RGPD3           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RGPD3 (see all 652)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs767502781,2
    C--106701596(-) CTGCAA/GTACAG 1 -- int10--------
    rs2020114001,2
    --106714132(-) ATTTT-/ATTTTT 1 -- int10--------
    rs3733320401,2
    C--106715624(-) TGGGTG/TAAGTG 1 -- int10--------
    rs2003481081,2
    C--106717628(-) GAGGCA/GGAAGA 1 -- int10--------
    rs1877339501,2
    --106718334(-) CCCTAC/TTGTGT 1 -- int10--------
    rs1825971201,2
    --106718347(-) AAAATA/GTAATA 1 -- int10--------
    rs1912216101,2
    --106718491(-) CTCTTC/GACATC 1 -- int10--------
    rs1859119651,2
    C--106718715(-) CAGGTG/TCCTGC 1 -- int10--------
    rs39541331,2
    C--106718943(-) caggcG/Atgagc 1 -- int11Minor allele frequency- A:0.50NA 2
    rs1815273131,2
    --106719032(-) GAGACA/GGAGTG 1 -- int10--------

    HapMap Linkage Disequilibrium report for RGPD3 (107021136 - 107084832 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for RGPD3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2720482CNV Deletion23290073
    esv1179092CNV Insertion17803354
    nsv834322CNV Gain17160897
    esv29426CNV Gain+Loss19812545

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 612706    OMIM disorders: --


    Find genes that share disorders with RGPD3           About GenesLikeMe


    Export disorders for RGPD3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for RGPD3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with RGPD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2, 3 Hillier L.W.... Wilson R.K. (Nature 2005)
    2. Complex genomic rearrangements lead to novel primate gene function. (PubMed id 15710750)1, 2, 3 Ciccarelli F.D.... Bork P. (Genome Res. 2005)
    3. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? (PubMed id 23314748)1 Nathan J.A....Goldberg A.L. (EMBO J. 2013)
    4. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    5. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    6. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    7. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    8. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 653489 HGNC: 32416 Ensembl:ENSG00000153165 euGenes: HUgn653489 ECgene: RGPD3
    H-InvDB: RGPD3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RGPD3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RGPD3 gene:
    Search GeneIP for patents involving RGPD3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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