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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RGPD6 Gene

protein-coding   GIFtS: 38
GCID: GC02M111271

RANBP2-Like And GRIP Domain Containing 6

  Search for RGPD6
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
RANBP2-Like And GRIP Domain Containing 61 2     RANBP2-Like And GRIP Domain-Containing Protein 5/62
RGP62 3 5     RANBP2-Like And GRIP Domain-Containing Protein 72
Ran-Binding Protein 2-Like 1/22 3     RANBP2L13
RanBP2-Like 1/22 3     RANBP2L23
RGPD72 3     RGP53
RanBP2L12 3     RGP73
RanBP2L22 3     Sperm Membrane Protein BS-633

External Ids:    HGNC: 324191   Entrez Gene: 7295402   Ensembl: ENSG000001830547   OMIM: 6127095   UniProtKB: Q996663   

Export aliases for RGPD6 gene to outside databases

Previous GC identifers: GC02U900804 GC02M110708


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for RGPD6 Gene: 
RGPD6 (RANBP2-like and GRIP domain containing 6) 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NT_022135.16  NC_018913.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RGPD6 gene promoter:
         IRF-1   Nkx2-5   MEF-2A   POU2F1   POU2F1a   aMEF-2   Pax-4a   Hlf   ATF6   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for RGPD6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RGPD6


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

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

RGPD6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RGPD6 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M111271:  view genomic region     (about GC identifiers)

Start:
111,271,379 bp from pter      End:
111,336,309 bp from pter
Size:
64,931 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RGPD5_HUMAN, Q99666 (See protein sequence)
Recommended Name: RANBP2-like and GRIP domain-containing protein 5/6  
Size: 1765 amino acids; 198924 Da
Subcellular location: Cytoplasm
Miscellaneous: One of the 8 copies of RANBP2 clustered close to the chromosome 2 centromere
Secondary accessions: Q53QN2 Q53T03 Q59GM7 Q9H0B2
Alternative splicing: 2 isoforms:  Q99666-1   Q99666-2   

Explore the universe of human proteins at neXtProt for RGPD6: NX_Q99666

Explore proteomics data for RGPD6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q99666

  • RGPD6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RGPD6 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001032955.1  NP_001116835.1  

    ENSEMBL proteins: 
     ENSP00000330842   ENSP00000387779   ENSP00000418549   ENSP00000330023   ENSP00000410084  
     ENSP00000409424  

    Human Recombinant Protein Products for RGPD6: 
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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for RGPD6 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--

    RGPD6 for ontologies           About GeneDecksing



    RGPD6 Antibody Products: 
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    Cloud-Clone Corp. CLIAs for RGPD6


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

    5/7 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 Q99666

    ProtoNet protein and cluster: Q99666

    1 Blocks protein domain: IPB000156 RanBP1 domain

    UniProtKB/Swiss-Prot: RGPD5_HUMAN, Q99666
    Similarity: Contains 1 GRIP domain
    Similarity: Contains 2 RanBD1 domains
    Similarity: Contains 3 TPR repeats


    RGPD6 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    RGPD6 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for RGPD6 
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RGPD6


    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RGPD6

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    5/15 Interacting proteins for RGPD6 (Q996663 ENSP000003308424) via UniProtKB, MINT, STRING, and/or I2D (see all 15)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000206289P287023I2D: score=1 
    ENSG00000227322P287023I2D: score=1 
    ENSG00000228333P287023I2D: score=1 
    ENSG00000231321P287023I2D: score=1 
    ENSG00000235712P287023I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

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

    RGPD6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RGPD6 (RGPD5)

    Search CenterWatch for drugs/clinical trials and news about RGPD6 / RGPD5

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RGPD6 gene (2 alternative transcripts): 
    NM_001037866.1  NM_001123363.3  

    Unigene Cluster for RGPD6:

    RANBP2-like and GRIP domain containing 6
    Hs.645445  [show with all ESTs]
    Unigene Representative Sequence: NM_001123363
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000463822 ENST00000329516(uc021vmh.1) ENST00000437167 ENST00000484024
    ENST00000330331(uc010yxg.2) ENST00000473101 ENST00000459645 ENST00000490990
    ENST00000446930 ENST00000480894 ENST00000455695
    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat RGPD6
    Search QIAGEN for miScript miRNA Assays for microRNAs that regulate RGPD6
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for RGPD6
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat RGPD6
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): RGPD6 (NM_001037866)
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RGPD6
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RGPD6

    Additional mRNA sequence: AK056675.1 

    12 DOTS entries:

    DT.120954962  DT.92416382  DT.120992096  DT.91900581  DT.75115124  DT.95274706  DT.92409447  DT.120954921 
    DT.120968018  DT.120992130  DT.120954978  DT.120968046 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RGPD6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    RGPD6 Expression
    About this image


    See RGPD6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RGPD6

    SOURCE GeneReport for Unigene cluster: Hs.645445

    UniProtKB/Swiss-Prot: RGPD5_HUMAN, Q99666
    Tissue specificity: Expressed in testis

        SABiosciences Custom PCR Arrays for RGPD6
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RGPD6

    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for RGPD6 gene from 5/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves PPIA6
    --
    (see all 5)
    --

    60(a)
    (see all 5)
    possible ortholog
    possible ortholog
    (see all 5)
    22(4060940-4061857)
    12(25698-75398)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein

    42(a)
    possible ortholog
    possible ortholog
    GL343238.1(667038-675712)
    3(107454117-107504389)
    zebrafish
    (Danio rerio)
    Actinopterygii RANBP2 (1 of 2)6
    RANBP2 (2 of 2)6
    RAN binding protein 2
    5(a)
    2(a)
    possible ortholog
    possible ortholog
    9(3151974-3165972)
    9(399379-423700)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG50716
    Nup3586
    Nucleoporin 358
    6(a)
    6(a)
    possible ortholog
    1 ↔ many
    3R(21444136-21446401)
    3R(21075316-21084394)
    worm
    (Caenorhabditis elegans)
    Secernentea Y17G9B.46
    T22F3.126
    (see all 3)
    Protein T22F3.12
    (see all 3)


    (see all 3)
    possible ortholog
    possible ortholog
    (see all 3)
    IV(4752094-4753230)
    V(3589029-3592199)
            Species with no ortholog for RGPD6

    ENSEMBL Gene Tree for RGPD6 (if available)
    TreeFam Gene Tree for RGPD6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RGPD6 gene
    RGPD51 2  RGPD81 2  RGPD31 2  RGPD41 2  RGPD11 2  RGPD21 2  PPIE2  PPIAL4C2  
    RANBP22  PPIF2  PPIA2  PPIAL4D2  PPIAL4A2  PPIAL4G2  PPIAL4B2  
    7 SIMAP similar genes for RGPD6 using alignment to 3 protein entries:     RGPD5_HUMAN (see all proteins):
    RGPD5    RGPD2    RGPD8    RGPD3    RGPD4    RGPD1
    RANBP2

    RGPD6 for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    7 SNPs in RGPD6 are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2018095381,2
    --111293488(+) TGAAT-/TAAGG 
            
    TATTA
    1 -- int10--------
    rs1417460441,2
    ----111305505(+) TCTCAA/GAAACA 2 -- int10--------
    rs1510790001,2
    ----111305527(+) GAAAAA/GAAAAG 2 -- int10--------
    rs3724975431,2
    ----111330093(+) GAGCC-/GCCAGT 2 -- int10--------
    rs3681949781,2
    ----110839811(-) CGGCG-/CGGGGG 2 -- int10--------
    rs1996356571,2
    ----111304748(+) GCAAAC/TGATGG 4 H R mis10--------
    rs1476791301,2
    ----111305509(+) AAAAAA/CAAGAA 2 -- int10--------

    HapMap Linkage Disequilibrium report for RGPD6 (111271379 - 111336309 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for RGPD6:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2751812CNV Loss17911159
    nsv508159CNV Loss20534489
    nsv874777CNV Gain21882294
    dgv4263n71CNV Gain21882294
    nsv510884CNV Complex20534489

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing RGPD6
    DNA2.0 Custom Variant and Variant Library Synthesis for RGPD6

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    RGPD6 for disorders           About MalaCards
    OMIM gene information: 612709    OMIM disorders: --


    RGPD6 for disorders           About GeneDecksing


    Export disorders for RGPD6 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)
    About This Section

    PubMed articles for RGPD6 gene, integrated from 9 sources (see all 14):
    (articles sorted by number of sources associating them with RGPD6)
        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. (2005)
    2. Complex genomic rearrangements lead to novel primate gene function. (PubMed id 15710750)1, 2, 3 Ciccarelli F.D.... Bork P. (2005)
    3. Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. (PubMed id 18220336)1, 2 Cantin G.T....Yates J.R. III (2008)
    4. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)1, 2 Dephoure N.... Gygi S.P. (2008)
    5. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (2001)
    6. Identification of a novel Ran binding protein 2 related gene (RANBP2L1) and detection of a gene cluster on human chromosome 2q11- q12. (PubMed id 9480752)1, 3 Nothwang H.G.... Hildebrandt F. (1998)
    7. The intracellular interactome of tetraspanin-enriched microdomains reveals their function as sorting machineries toward exosomes. (PubMed id 23463506)1 Perez-Hernandez D....Yanez-Mo M. (2013)
    8. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    9. Systematic analysis of human protein complexes identi fies chromosome segregation proteins. (PubMed id 20360068)1 Hutchins J.R....Peters J.M. (2010)
    10. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. (PubMed id 18691976)2 Daub H.... Mann M. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 729540 HGNC: 32419 Ensembl:ENSG00000183054 euGenes: HUgn729540 ECgene: RGPD6
    H-InvDB: RGPD6

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RGPD6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RGPD6 gene:
    Search GeneIP for patents involving RGPD6

    GeneCards and IP:
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    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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