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RGPD6 Gene

protein-coding   GIFtS: 38
GCID: GC02M111271

RANBP2-Like And GRIP Domain Containing 6

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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 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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   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 Chromatin IP Primers for RGPD6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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: RGPD5_HUMAN, Q99666 (See protein sequence)
Recommended Name: RANBP2-like and GRIP domain-containing protein 5/6  
Size: 1765 amino acids; 198924 Da
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: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RGPD6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000330842   ENSP00000387779   ENSP00000418549   ENSP00000330023   ENSP00000410084  
     ENSP00000409424  

    RGPD6 Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for RGPD6
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    Cloud-Clone Corp. Proteins for RGPD6

     
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    antibodies-online antibodies for RGPD6 

    RGPD6 Assay Products:

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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 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


    Find genes that share domains with RGPD6           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 RGPD6           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RGPD6

    miRNA
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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 UniProtKB/Swiss-Prot
    RGPD5_HUMAN, Q99666: Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    mitochondrion1
    nucleus1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    Find genes that share ontologies with RGPD6           About GenesLikeMe


    (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 RGPD6
    Interactions:

        Search GeneGlobe Interaction Network for RGPD6

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

    Selected Interacting proteins for RGPD6 (Q996663 ENSP000003308424) via UniProtKB, MINT, STRING, and/or I2D (see all 38)
    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:    About this table

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

    Find genes that share ontologies with RGPD6           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 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,
    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 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
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    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat RGPD6
      QuantiTect SYBR Green Assays in human, mouse, rat RGPD6
      QuantiFast Probe-based Assays in human, mouse, rat RGPD6

    Additional mRNA sequence: AK056675.1 

    12 DOTS entries:

    DT.120954962  DT.120992096  DT.92416382  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™, 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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    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

    RGPD6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RGPD6 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.645445

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

        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)
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    This gene was present in the common ancestor of animals.

    Orthologs for RGPD6 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ranbp21 RAN binding protein 2 87.56(n)
    88.11(a)
      19386  NM_011240.3  NP_035370.2 
    chicken
    (Gallus gallus)
    Aves RANBP21 RAN binding protein 2 70.83(n)
    68.66(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 66.47(n)
    62.47(a)
      100134999  XM_002937658.2  XP_002937704.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch1073-55a19.21 si:ch1073-55a19.2 56.16(n)
    54.69(a)
      100317326  XM_005169115.1  XP_005169172.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG50716
    --
    15(a)
    1 → many
    3R(21444136-21446401)
    worm
    (Caenorhabditis elegans)
    Secernentea T22F3.126
    Y17G9B.46
    Protein Y17G9B.4 (Y17G9B.4) mRNA, complete cds
    9(a)
    13(a)
    many ↔ many
    many ↔ many
    V(3589029-3592199) WBGene00044705
    IV(4752094-4753230) WBGene00021201


    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)
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    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

    Find genes that share paralogs with RGPD6           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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    7 SNPs for RGPD6    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

    Site Specific Mutation Identification with 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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 612709    OMIM disorders: --


    Find genes that share disorders with RGPD6           About GenesLikeMe


    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)
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    PubMed articles for RGPD6 gene, integrated from 10 sources (see all 15):
    (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. (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. 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 (J. Proteome Res. 2008)
    4. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)1, 2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 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. (Genome Res. 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. (Genomics 1998)
    7. The intracellular interactome of tetraspanin-enriched microdomains reveals their function as sorting machineries toward exosomes. (PubMed id 23463506)1 Perez-Hernandez D....YA!A+ez-MA^ M. (J. Biol. Chem. 2013)
    8. 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)
    9. Systematic analysis of human protein complexes identifies chromosome segregation proteins. (PubMed id 20360068)1 Hutchins J.R.... Peters J.M. (Science 2010)
    10. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. (PubMed id 18691976)2 Daub H.... Mann M. (Mol. Cell 2008)

    (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: 729540 HGNC: 32419 Ensembl:ENSG00000183054 euGenes: HUgn729540 ECgene: RGPD6
    H-InvDB: RGPD6

    (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 RGPD6 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 RGPD6 gene:
    Search GeneIP for patents involving RGPD6

    GeneCards and IP:
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    (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
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     Block miRNA regulation of human, mouse, rat RGPD6 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing RGPD6
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