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RHBDD3 Gene

protein-coding   GIFtS: 50
GCID: GC22M029655

Rhomboid Domain Containing 3

(Previous name: chromosome 22 open reading frame 3)
(Previous symbol: C22orf3)
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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
Rhomboid Domain Containing 31 2     PTAG2
C22orf31 2 3     Pituitary Tumor Apoptosis2
Chromosome 22 Open Reading Frame 31     Rhomboid Domain-Containing Protein 32
HS984G1A2     

External Ids:    HGNC: 13081   Entrez Gene: 258072   Ensembl: ENSG000001002637   UniProtKB: Q9Y3P43   

Export aliases for RHBDD3 gene to outside databases

Previous GC identifers: GC22M027985 GC22M012620


(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 RHBDD3 Gene:
RHBDD3 (rhomboid domain containing 3) is a protein-coding gene. GO annotations related to this gene include serine-type endopeptidase activity.


(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  NT_011520.13  NC_018933.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RHBDD3 gene promoter:
         AML1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRHBDD3 promoter sequence
   Search Chromatin IP Primers for RHBDD3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RHBDD3


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

Entrez Gene cytogenetic band: 22q12.2   Ensembl cytogenetic band:  22q12.2   HGNC cytogenetic band: 22q12.2

RHBDD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RHBDD3 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M029655:  view genomic region     (about GC identifiers)

Start:
29,655,841 bp from pter      End:
29,664,198 bp from pter
Size:
8,358 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: RHBD3_HUMAN, Q9Y3P4 (See protein sequence)
Recommended Name: Rhomboid domain-containing protein 3  
Size: 386 amino acids; 40484 Da
Secondary accessions: Q6I9X3 Q9UGQ7

Explore the universe of human proteins at neXtProt for RHBDD3: NX_Q9Y3P4

Explore proteomics data for RHBDD3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys374
  • Modification sites at PhosphoSitePlus

  • See RHBDD3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_036397.1  
    ENSEMBL proteins: 
     ENSP00000216085   ENSP00000399550   ENSP00000413128   ENSP00000384113  

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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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    2 InterPro protein domains:
     IPR022764 Peptidase_S54_rhomboid_dom
     IPR009060 UBA-like

    Graphical View of Domain Structure for InterPro Entry Q9Y3P4

    ProtoNet protein and cluster: Q9Y3P4

    2 Blocks protein domains:
    IPB000449 Ubiquitin-associated domain
    IPB002610 Rhomboid-like protein


    UniProtKB/Swiss-Prot: RHBD3_HUMAN, Q9Y3P4
    Similarity: Contains 1 UBA domain


    Find genes that share domains with RHBDD3           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): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004252serine-type endopeptidase activity IEA--
    GO:0005515protein binding ----
         
    Find genes that share ontologies with RHBDD3           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for RHBDD3:
     Increased gamma-H2AX phosphory 

         5 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rhbdd3):
     hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system  mortality/aging 

    Find genes that share phenotypes with RHBDD3           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Rhbdd3tm1Caox for RHBDD3

       genOway: Develop your customized and physiologically relevant rodent model for RHBDD3

    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
    RHBD3_HUMAN, Q9Y3P4: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane2
    cytoskeleton1
    endoplasmic reticulum1
    extracellular1
    lysosome1
    mitochondrion1
    nucleus1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with RHBDD3           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 RHBDD3
    Interactions:

        Search GeneGlobe Interaction Network for RHBDD3

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for RHBDD3 (Q9Y3P43 ENSP000002160854) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    About this table

    (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 RHBDD3 (RHBD3)



    (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 RHBDD3 gene: 
    NM_012265.1  

    Unigene Cluster for RHBDD3:

    Rhomboid domain containing 3
    Hs.106730  [show with all ESTs]
    Unigene Representative Sequence: AL050346
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000216085(uc003aeq.1) ENST00000413137 ENST00000496342 ENST00000414672
    ENST00000406335 ENST00000493894 ENST00000488106
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      QuantiFast Probe-based Assays in human, mouse, rat RHBDD3

    Additional mRNA sequence: 

    AL050346.1 BC002705.2 BC018872.2 CR456411.1 CR457382.1 

    14 DOTS entries:

    DT.442630  DT.95355299  DT.100693816  DT.100813922  DT.100705718  DT.100776318  DT.120631417  DT.100700112 
    DT.40195915  DT.92068734  DT.95373894  DT.97845425  DT.406573  DT.100833847 

    Selected AceView cDNA sequences (see all 184):

    AI675187 CR593733 BQ636566 BQ053724 AW087238 AA423827 BQ893569 NM_012265 
    AA284627 AI222511 AL050346 BM981011 BM682569 AI687772 CK821673 F25808 
    CF529639 CR606788 CB049483 BQ918247 CB049484 BQ778252 BI791513 BE645104 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for RHBDD3 (see all 8)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9
    SP1:                          -           -           -     -                       -     -                           
    SP2:        -     -     -     -           -           -     -                                                         
    SP3:                          -           -           -     -     -     -     -                                       
    SP4:                          -           -                                                                           
    SP5:                                      -           -     -                                                         


    ECgene alternative splicing isoforms for RHBDD3

    (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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    RHBDD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGCCCTAGT
    RHBDD3 Expression
    About this image

    RHBDD3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RHBDD3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.106730
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    In Situ
    Assay Products:
     

     
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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 chordates.

    Orthologs for RHBDD3 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rhbdd31 , 5 rhomboid domain containing 31, 5 79.46(n)1
    76.24(a)1
      11 (3.26 cM)5
    2797661  NM_177370.31  NP_796344.11 
     50989265 
    lizard
    (Anolis carolinensis)
    Reptilia RHBDD36
    rhomboid domain containing 3
    42(a)
    1 ↔ 1
    GL343417.1(114303-116663)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia rhbdd31 rhomboid domain containing 3 46.47(n)
    36.52(a)
      733768  NM_001044516.1  NP_001037981.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rhbdd36
    rhomboid domain containing 3
    32(a)
    1 ↔ 1
    5(26551568-26555532) ENSDARG00000079816


    ENSEMBL Gene Tree for RHBDD3 (if available)
    TreeFam Gene Tree for RHBDD3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RHBDD3 gene
    7 SIMAP similar genes for RHBDD3 using alignment to 4 protein entries:     RHBD3_HUMAN (see all proteins):
    ABCG5    NCF1    PAM16    MRPS28    HK1    NAA15
    ADCY7

    Find genes that share paralogs with RHBDD3           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 RHBDD3 (see all 172)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs22313991,2
    C,H--29656145(-) GGTGCC/TGTGTC 2 A syn1 ese34Minor allele frequency- T:0.00NS EA 420
    rs2020887671,2
    --29656159(+) CACACA/GGCCTG 2 R C mis10--------
    rs1133625091,2
    C--29656165(+) GCCTGC/TGGCTG 2 T A mis11Minor allele frequency- T:0.00CSA 1
    rs2013174731,2
    --29656171(+) GGCTGC/TCAGTG 2 T A mis10--------
    rs2012297761,2
    C--29656179(+) GTGCCA/CCCACC 2 G V mis10--------
    rs2005415821,2
    --29656209(+) CCATGC/TGCTCC 2 H R mis10--------
    rs1996339361,2
    --29656238(+) GGGGTC/GGGGGG 1 -- int10--------
    rs1152863571,2
    C--29656240(+) GGTGGG/AGGGAG 1 -- int11Minor allele frequency- A:0.01WA 118
    rs1866881761,2
    C--29656251(+) AAGTGG/TGGAGT 1 -- int11Minor allele frequency- T:0.01EU 171
    rs2015728071,2
    --29656253(+) GTGGGA/GAGTGT 1 -- int10--------

    HapMap Linkage Disequilibrium report for RHBDD3 (29655841 - 29664198 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for RHBDD3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv834171CNV Loss17160897
    nsv829154CNV Gain20364138

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RHBDD3
    DNA2.0 Custom Variant and Variant Library Synthesis for RHBDD3

    (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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      --

    (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 RHBDD3 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with RHBDD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 2, 3 Dunham I.... Wright H. (Nature 1999)
    2. Isolation and characterization of a novel pituitary tumor apoptosis gene. (PubMed id 15105437)1, 3, 9 Bahar A....Farrell W.E. (Mol. Endocrinol. 2004)
    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. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (Genome Biol. 2004)
    5. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. (PubMed id 12529303)1, 2 Collins J.E.... Dunham I. (Genome Res. 2003)
    6. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. (PubMed id 23535729)1 Michailidou K....Easton D.F. (Nat. Genet. 2013)
    7. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    8. The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. (PubMed id 21555518)1 Warnatz H.J....Yaspo M.L. (J. Biol. Chem. 2011)
    9. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)
    10. Bidirectionality and transcriptional activity of the EWSR1 promoter region. (PubMed id 19212622)1 MAPller E....Panagopoulos I. (Oncol. Rep. 2009)

    (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: 25807 HGNC: 1308 AceView: C22orf3 Ensembl:ENSG00000100263 euGenes: HUgn25807
    ECgene: RHBDD3 H-InvDB: RHBDD3

    (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 RHBDD3 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 RHBDD3 gene:
    Search GeneIP for patents involving RHBDD3

    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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