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RIMBP3 Gene

protein-coding   GIFtS: 44
GCID: GC22M020456

RIMS Binding Protein 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
RIMS Binding Protein 31 2     RIM-BP32
RIMBP3A2 3 5     RIMBP3.12
RIM-BP3.12 3     RIMS Binding Protein 3.12
RIM-BP3.A2 3     RIMS-Binding Protein 3A2
KIAA16663 5     RIMS-Binding Protein 3.13

External Ids:    HGNC: 293441   Entrez Gene: 853762   Ensembl: ENSG000001966227   OMIM: 6126995   UniProtKB: Q9UFD93   

Export aliases for RIMBP3 gene to outside databases

Previous GC identifers: GC22M018843 GC22M003946


(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 RIMBP3 Gene:
RIMBP3 (RIMS binding protein 3) is a protein-coding gene. An important paralog of this gene is RIMBP3B.


(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_000022.10  NC_018933.2  NT_187357.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the RIMBP3 gene promoter:
         ER-alpha   USF1   Brachyury   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   Egr-2   SRY   COMP1   USF-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RIMBP3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RIMBP3


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

Entrez Gene cytogenetic band: 22q11.21   Ensembl cytogenetic band:  22q11.21   HGNC cytogenetic band: 22q11.21

RIMBP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RIMBP3 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M020456:  view genomic region     (about GC identifiers)

Start:
20,455,991 bp from pter      End:
20,461,786 bp from pter
Size:
5,796 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: RIM3A_HUMAN, Q9UFD9 (See protein sequence)
Recommended Name: RIMS-binding protein 3A  
Size: 1639 amino acids; 180717 Da
Sequence caution: Sequence=AAH35246.2; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAB33336.1; Type=Frameshift; Positions=652; Sequence=CAB61362.2; Type=Erroneous initiation;
Note=Translation N-terminally extended;
1 PDB 3D structure from and Proteopedia for RIMBP3:
2EGE (3D)    
Secondary accessions: Q8IYP7 Q9BY94 Q9UFQ5

Explore the universe of human proteins at neXtProt for RIMBP3: NX_Q9UFD9

Explore proteomics data for RIMBP3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys1226
  • Modification sites at PhosphoSitePlus

  • See RIMBP3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_056487.1  
    ENSEMBL proteins: 
     ENSP00000391564  

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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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    4 InterPro protein domains:
     IPR003961 Fibronectin_type3
     IPR001452 SH3_domain
     IPR013783 Ig-like_fold
     IPR011511 SH3_2

    Graphical View of Domain Structure for InterPro Entry Q9UFD9

    ProtoNet protein and cluster: Q9UFD9

    1 Blocks protein domain: IPB011511 Variant SH3

    UniProtKB/Swiss-Prot: RIM3A_HUMAN, Q9UFD9
    Similarity: Belongs to the RIMBP family
    Similarity: Contains 2 fibronectin type-III domains
    Similarity: Contains 3 SH3 domains


    Find genes that share domains with RIMBP3           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 RIMBP3           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RIMBP3

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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
    nucleus3
    cytosol2
    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 RIMBP3
    Interactions:

        Search GeneGlobe Interaction Network for RIMBP3

    (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
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    Browse Tocris compounds for RIMBP3 (RIM3A)



    (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 RIMBP3 gene: 
    NM_015672.1  

    Unigene Cluster for RIMBP3:

    RIMS binding protein 3
    Hs.115429  [show with all ESTs]
    Unigene Representative Sequence: NM_015672
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000426804(uc002zsd.4)
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    Additional mRNA sequence: 

    AB051453.1 AL117509.1 AL133030.1 BC035246.1 

    4 DOTS entries:

    DT.95295994  DT.120629490  DT.411088  DT.95092771 

    Selected AceView cDNA sequences (see all 29):

    AI014598 AA782009 BU738457 AI240644 AA973051 AL133030 AA813520 AW958311 
    BV193891 BV189191 AL117509 BV193887 AB051453 BV176571 BV197087 BV197086 
    BV193892 AL041043 AW172455 AW086440 BM712850 BV193890 BC035246 BG723046 

    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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    RIMBP3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGCGTCCCTC
    RIMBP3 Expression
    About this image

    RIMBP3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RIMBP3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.115429
        Custom PCR Arrays for RIMBP3
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    In Situ
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    (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 RIMBP3 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rimbp31 RIMS binding protein 3 73.68(n)
    64.92(a)
      239731  NM_001033338.3  NP_001028510.2 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    30(a)
    many ↔ many
    AADN03022212.1(18873-20179)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    37(a)
    1 → many
    GL343312.1(18496-22269)
    zebrafish
    (Danio rerio)
    Actinopterygii rimbp26
    RIMS binding protein 2
    4(a)
    many ↔ many
    8(46121698-46125794) ENSDARG00000093752
    fruit fly
    (Drosophila melanogaster)
    Insecta Rbp6
    RIM-binding protein
    13(a)
    1 → many
    3R(11200424-11228265)
    worm
    (Caenorhabditis elegans)
    Secernentea tag-1686
    Protein TAG-168 (tag-168) mRNA, complete cds
    16(a)
    1 → many
    III(1789147-1806621) WBGene00006513


    ENSEMBL Gene Tree for RIMBP3 (if available)
    TreeFam Gene Tree for RIMBP3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RIMBP3 gene
    RIMBP3B1 2  RIMBP3C1 2  BZRAP12  RIMBP22  
    2 SIMAP similar genes for RIMBP3 using alignment to 1 protein entry:     RIM3A_HUMAN:
    RIMBP3B    RIMBP3C

    Find genes that share paralogs with RIMBP3           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 RIMBP3 (see all 175)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3718188631,2
    C--3953475(+) ATATAA/CTATGT 1 -- us2k10--------
    rs3739933541,2
    C--3953627(+) CATATA/GTATAA 1 -- us2k10--------
    rs1808446661,2
    --3953645(+) ATTATA/GTATAA 1 -- us2k10--------
    rs1399078771,2
    --3953703(+) TATATC/TACATA 1 -- us2k10--------
    rs3752498871,2
    C--3953728(+) TTATA-/TAATATA 1 -- us2k10--------
    rs2009893651,2
    --3953831(+) ATACA-/AT    
       ATAAT
    ATATA
    1 -- us2k10--------
    rs1910393811,2
    --3953839(+) TAATAC/TATAAT 1 -- us2k10--------
    rs96128841,2
    --3953843(+) atataA/Ttatat 1 -- us2k10--------
    rs1879494971,2
    --3953892(+) ATATAA/TATTAT 1 -- us2k10--------
    rs1905221171,2
    --3953911(+) ATATTA/TTATAT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RIMBP3 (20455991 - 20461786 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for RIMBP3 (see all 14):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv817e199CNV Deletion23128226
    nsv435744CNV Deletion17901297
    nsv820540CNV Duplication20802225
    dgv16n31CNV Duplication19718026
    nsv436867CNV Insertion17901297
    nsv510803CNV Loss20534489
    esv33990CNV Loss17666407
    nsv914377CNV Gain21882294
    nsv914378CNV Gain21882294
    dgv4866n71CNV Gain21882294

    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: 612699    OMIM disorders: --


    Find genes that share disorders with RIMBP3           About GenesLikeMe


    Export disorders for RIMBP3 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 RIMBP3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with RIMBP3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of novel transcribed sequences on human chromosome 22 by expressed sequence tag mapping. (PubMed id 11258795)1, 2, 3 Hirosawa M.... Ohara O. (DNA Res. 2001)
    2. Structure and evolution of RIM-BP genes: identification of a novel family member. (PubMed id 17855024)1, 3 Mittelstaedt T. and Schoch S. (Gene 2007)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 2 Dunham I.... Wright H. (Nature 1999)
    5. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. (PubMed id 23128233)1 Jostins L....Cho J.H. (Nature 2012)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    7. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 85376 HGNC: 29344 AceView: LOC150221 Ensembl:ENSG00000196622 euGenes: HUgn85376
    ECgene: RIMBP3 H-InvDB: RIMBP3

    (According to HUGE)
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    HUGE: KIAA1666

    (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 RIMBP3 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 RIMBP3 gene:
    Search GeneIP for patents involving RIMBP3

    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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