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RGPD5 Gene

protein-coding   GIFtS: 48
GCID: GC02P110550

RANBP2-Like And GRIP Domain Containing 5

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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 51 2     RanBP2-Like 12
RGP52 3 5     RANBP2-Like And GRIP Domain-Containing Protein 52
Ran-Binding Protein 2-Like 1/22 3     RANBP2-Like And GRIP Domain-Containing Protein 5/62
RanBP2-Like 1/22 3     RANBP2L13
Sperm Membrane Protein BS-632 3     RANBP2L23
BS632 5     RGP63
BS-632     RGP73
HEL1612     RGPD73
Epididymis Luminal Protein 1612     RanBP2L13
Ran-Binding Protein 2-Like 12     RanBP2L23
ranBP2L12     

External Ids:    HGNC: 324181   Entrez Gene: 842202   Ensembl: ENSG000000155687   OMIM: 6127085   UniProtKB: Q996663   

Export aliases for RGPD5 gene to outside databases

Previous GC identifer: GC02P109908


(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 RGPD5 Gene:
RAN is a small GTP-binding protein of the RAS superfamily that is associated with the nuclear membrane and is
thought to control a variety of cellular functions through its interactions with other proteins. This gene shares
a high degree of sequence identity with RANBP2, a large RAN-binding protein localized at the cytoplasmic side of
the nuclear pore complex. It is believed that this RANBP2 gene family member arose from a duplication event 3 Mb
distal to RANBP2. Alternative splicing has been observed for this locus and two variants are described.
Additional splicing is suggested but complete sequence for further transcripts has not been determined. (provided
by RefSeq, Jul 2008)

GeneCards Summary for RGPD5 Gene:
RGPD5 (RANBP2-like and GRIP domain containing 5) is a protein-coding gene. An important paralog of this gene is PPIE.

Gene Wiki entry for RGPD5 Gene


(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  
Regulatory elements:
   Regulatory transcription factor binding sites in the RGPD5 gene promoter:
         POU2F1   Nkx2-5   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): RGPD5 promoter sequence
   Search Chromatin IP Primers for RGPD5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RGPD5


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

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

RGPD5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RGPD5 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P110550:  view genomic region     (about GC identifiers)

Start:
110,550,335 bp from pter      End:
110,615,272 bp from pter
Size:
64,938 bases      Orientation:
plus 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 RGPD5: NX_Q99666

Explore proteomics data for RGPD5 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys106, Lys1085, Lys1180, Lys1205, Lys1382, Lys1420, Lys1448
  • Modification sites at PhosphoSitePlus

  • See RGPD5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_005045.2  NP_115636.1  

    ENSEMBL proteins: 
     ENSP00000376962   ENSP00000392556   ENSP00000016946   ENSP00000411548   ENSP00000400797  
     ENSP00000409406   ENSP00000272454  

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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 RGPD5           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 RGPD5           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RGPD5

    miRNA
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    miRTarBase miRNAs that target RGPD5:
    hsa-mir-15a-5p (MIRT051322), hsa-mir-93-3p (MIRT038772)

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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 ----

    Find genes that share ontologies with RGPD5           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 RGPD5
    Interactions:

        GeneGlobe Interaction Network for RGPD5

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

    Selected Interacting proteins for RGPD5 (Q996663 ENSP000000169464) via UniProtKB, MINT, STRING, and/or I2D (see all 43)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000206289P287023I2D: score=1 
    ENSG00000227322P287023I2D: score=1 
    ENSG00000228333P287023I2D: score=1 
    ENSG00000231321P287023I2D: score=1 
    ENSG00000235712P287023I2D: score=1 
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    Gene Ontology (GO): 2 biological process terms:    About this table

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

    Find genes that share ontologies with RGPD5           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 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 RGPD5 gene (2 alternative transcripts): 
    NM_005054.2  NM_032260.2  

    Unigene Cluster for RGPD5:

    RANBP2-like and GRIP domain containing 5
    Hs.469630  [show with all ESTs]
    Unigene Representative Sequence: NM_005054
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000393283(uc002tfc.3) ENST00000430736 ENST00000016946(uc021vly.1)
    ENST00000441344 ENST00000432606 ENST00000482778 ENST00000472794 ENST00000413468
    ENST00000495473 ENST00000493394 ENST00000495582 ENST00000477523 ENST00000272454

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    Primer
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    Additional mRNA sequence: 

    AB209082.1 AL136868.1 BC020901.1 U64675.2 

    Selected DOTS entries (see all 47):

    DT.91900581  DT.92409447  DT.95274706  DT.95274721  DT.75115124  DT.92416382  DT.120954962  DT.120968086 
    DT.120954930  DT.120954977  DT.120968033  DT.86858214  DT.92453557  DT.120933586  DT.120968027  DT.91842999 
    DT.120954927  DT.120968053  DT.120992108  DT.120996976  DT.40118677  DT.120933571  DT.120933599  DT.120954978 

    Selected AceView cDNA sequences (see all 217):

    BQ000138 BE676452 CR626604 AF012086 CA449195 CA406479 BX281472 AA347163 
    AA081971 AW440914 AA972133 AL043480 BQ695350 AI124636 CA437157 N67549 
    AA649886 AI301579 CD675459 AI283773 CA446006 AA565297 AV645489 AI630782 

    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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    RGPD5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTTTCTGCAA
    RGPD5 Expression
    About this image

    RGPD5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RGPD5 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.469630

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

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RGPD5

    (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 RGPD5 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 87.56(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 RGPD5 (if available)
    TreeFam Gene Tree for RGPD5 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RGPD5 gene
    RGPD61 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 RGPD5 using alignment to 4 protein entries:     RGPD5_HUMAN (see all proteins):
    RGPD6    RGPD2    RGPD8    RGPD3    RGPD4    RGPD1
    RANBP2

    Find genes that share paralogs with RGPD5           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 RGPD5 (see all 15)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2007294351,2
    --110572433(+) TAAGC-/AGTCTTCC 2 -- int10--------
    rs2020593351,2
    --110578147(+) TTCCC-/TTTTCT 2 -- int10--------
    rs2000060641,2
    --110587145(+) GAGCA-/CTAGTC 2 -- int10--------
    rs2010839171,2
    --110602386(+) GATGG-/GAAGAAGA 1 -- int10--------
    rs2017876781,2
    --110602918(+) AGATG-/CATCTA 1 -- int10--------
    rs1902509461,2
    ----110568428(+) ATTTTG/TTTTGT 2 -- int10--------
    rs1429251621,2
    ----110576834(-) ACTGCA/GCCATT 2 -- int10--------
    rs284788631,2
    ----110552127(+) GGTCTC/GGAAGA 2 -- int10--------
    rs3755469251,2
    ----110615451(+) CATCC-/AAGCTA 1 -- ds50010--------
    rs2004940161,2
    ----110613935(+) TACTTG/TGGGAG 1 -- ut310--------

    HapMap Linkage Disequilibrium report for RGPD5 (110550335 - 110615272 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for RGPD5:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2720536CNV Deletion23290073
    esv2751812CNV Loss17911159
    nsv874863CNV Loss21882294
    nsv508159CNV Loss20534489
    nsv874777CNV Gain21882294
    dgv4263n71CNV Gain21882294
    nsv874871CNV Gain21882294
    nsv510884CNV Complex20534489

    Site Specific Mutation Identification with PCR Assays
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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: 612708    OMIM disorders: --


    Find genes that share disorders with RGPD5           About GenesLikeMe


    Export disorders for RGPD5 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 RGPD5 gene, integrated from 10 sources (see all 20):
    (articles sorted by number of sources associating them with RGPD5)
        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. Molecular cloning and characterization of a novel testis-specific nucleoporin-related gene. (PubMed id 10101573)1, 2, 9 Wang L.F....Koide S.S. (Arch. Androl. 1999)
    4. 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)
    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. 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)
    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. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
    9. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    10. 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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    Aliases
    Free Text  

      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 84220 HGNC: 32418 AceView: RANBP2L1.2 Ensembl:ENSG00000015568 euGenes: HUgn84220
    ECgene: RGPD5 H-InvDB: RGPD5

    (According to HUGE)
    About This Section

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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)
    About This Section

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    NameDescription
    PharmGKB entry for RGPD5 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 RGPD5 gene:
    Search GeneIP for patents involving RGPD5

    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
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