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

RHBDL3 Gene

protein-coding   GIFtS: 44
GCID: GC17P030593

Rhomboid, Veinlet-Like 3 (Drosophila)

(Previous names: rhomboid, veinlet-like 4 (Drosophila))
(Previous symbol: RHBDL4)
  Search for RHBDL3
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
Rhomboid, Veinlet-Like 3 (Drosophila)1 2     EC 3.4.21.1053 8
RHBDL41 2 3     Rhomboid, Veinlet-Like 4 (Drosophila)1
Ventrhoid Transmembrane Protein2 3     Rhomboid, Veinlet-Like 42
VRHO2 3     Rhomboid-Related Protein 32

External Ids:    HGNC: 165021   Entrez Gene: 1624942   Ensembl: ENSG000001413147   UniProtKB: P588723   

Export aliases for RHBDL3 gene to outside databases

Previous GC identifers: GC00U991136 GC17P027618 GC17P026782


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

GeneCards Summary for RHBDL3 Gene: 
RHBDL3 (rhomboid, veinlet-like 3 (Drosophila)) is a protein-coding gene. GO annotations related to this gene include serine-type endopeptidase activity and calcium ion binding. An important paralog of this gene is RHBDL2.

UniProtKB/Swiss-Prot: RHBL3_HUMAN, P58872
Function: May be involved in regulated intramembrane proteolysis and the subsequent release of functional
polypeptides from their membrane anchors (By similarity)




(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_000017.10  NT_010799.15  NC_018928.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RHBDL3 gene promoter:
         STAT1   NF-1   p53   NRSF form 1   STAT1beta   STAT5A   NRSF form 2   STAT1alpha   POU2F1   HOXA5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRHBDL3 promoter sequence
   Search SABiosciences Chromatin IP Primers for RHBDL3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RHBDL3


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

Entrez Gene cytogenetic band: 17q11.2   Ensembl cytogenetic band:  17q11.2   HGNC cytogenetic band: 17q11.2

RHBDL3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RHBDL3 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P030593:  view genomic region     (about GC identifiers)

Start:
30,593,195 bp from pter      End:
30,651,680 bp from pter
Size:
58,486 bases      Orientation:
plus 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: RHBL3_HUMAN, P58872 (See protein sequence)
Recommended Name: Rhomboid-related protein 3  
Size: 404 amino acids; 45245 Da
Subcellular location: Membrane; Multi-pass membrane protein (Probable)
Secondary accessions: A6NMH1 Q495Y6

Explore the universe of human proteins at neXtProt for RHBDL3: NX_P58872

Explore proteomics data for RHBDL3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P58872

  • 2 DME Specific Peptides for RHBDL3 (P58872)
     GRAVWLRF  GVPLEMVHG 

    RHBDL3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RHBDL3 Protein Expression
    REFSEQ proteins: NP_612201.1  
    ENSEMBL proteins: 
     ENSP00000463941   ENSP00000394849   ENSP00000269051   ENSP00000442092   ENSP00000466508  

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--

    RHBDL3 for ontologies           About GeneDecksing



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

    5 InterPro protein domains:
     IPR011992 EF-hand-like_dom
     IPR002048 EF_hand_dom
     IPR022764 Peptidase_S54_rhomboid_dom
     IPR002610 Peptidase_S54_rhomboid
     IPR017213 Peptidase_S54_rhomboid_met

    Graphical View of Domain Structure for InterPro Entry P58872

    ProtoNet protein and cluster: P58872

    1 Blocks protein domain: IPB002610 Rhomboid-like protein

    UniProtKB/Swiss-Prot: RHBL3_HUMAN, P58872
    Similarity: Belongs to the peptidase S54 family
    Similarity: Contains 2 EF-hand domains


    RHBDL3 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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RHBL3_HUMAN, P58872
    Function: May be involved in regulated intramembrane proteolysis and the subsequent release of functional
    polypeptides from their membrane anchors (By similarity)
    Catalytic activity: Cleaves type-1 transmembrane domains using a catalytic dyad composed of serine and histidine
    that are contributed by different transmembrane domains

         Enzyme Number (IUBMB): EC 3.4.21.1051 2

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004252serine-type endopeptidase activity IEA--
    GO:0005509calcium ion binding IEA--
         
    RHBDL3 for ontologies           About GeneDecksing


    Animal Models:
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    (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 RHBDL3

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

    5/12 Interacting proteins for RHBDL3 (P588723 ENSP000002690514) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BMP4P126443I2D: score=1 
    CHRDQ9H2X03I2D: score=1 
    CTNNB1P352223I2D: score=1 
    ETV6P412123I2D: score=1 
    FRKP426853I2D: score=1 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006508proteolysis IEA--

    RHBDL3 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 RHBDL3 (RHBL3)

    Search CenterWatch for drugs/clinical trials and news about RHBDL3 / RHBL3

    (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 RHBDL3 gene: 
    NM_138328.2  

    Unigene Cluster for RHBDL3:

    Rhomboid, veinlet-like 3 (Drosophila)
    Hs.655027  [show with all ESTs]
    Unigene Representative Sequence: NM_138328
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000578006 ENST00000431505 ENST00000269051(uc002hhe.1 uc010csw.1 uc010csx.1 uc010csy.1)
    ENST00000538145 ENST00000536287(uc002hhf.1) ENST00000582967
    miRNA
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    hsa-miR-3685 hsa-miR-1321 hsa-miR-330-5p hsa-miR-3162-5p hsa-miR-3667-5p hsa-miR-124 hsa-miR-629* hsa-miR-326
    SwitchGear 3'UTR luciferase reporter plasmidRHBDL3 3' UTR sequence
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    Additional mRNA sequence: 

    AJ313480.1 AK124570.1 AK127490.1 AL133573.1 BC016953.1 BC100975.1 BC100976.1 BC100977.1 
    BC100978.1 BX647302.1 

    6 DOTS entries:

    DT.40115544  DT.112050  DT.92031890  DT.120900932  DT.75115271  DT.95079942 

    24/46 AceView cDNA sequences (see all 46):

    BE220111 NM_138328 BM674460 T16542 AA235710 BM695873 AI859187 BC016953 
    AJ313480 AI369789 AK124570 BM988137 AI197876 AK127490 BM717083 BX647302 
    BE904095 BE047684 BU731277 BM694767 BE221904 AA351652 BF447694 AI694520 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for RHBDL3    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b
    SP1:        -     -           -                                                         
    SP2:                                                                                    
    SP3:              -     -     -                                                         
    SP4:                          -           -                                             


    ECgene alternative splicing isoforms for RHBDL3

    (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

    RHBDL3 expression in normal human tissues (normalized intensities)      RHBDL3 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGCTCCCCG
    RHBDL3 Expression
    About this image


    RHBDL3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/3 selected tissues (see all 3) fully expand
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Roof Plate Cells Mesencephalic Roof Plate
             Mesencephalic Roof Plate
     
     Eye (Sensory Organs)
             Human Lens Epithelial Cells (HLEpiC)   
     
     Epithelium (Uncategorized)
             Human Lens Epithelial Cells (HLEpiC)   

    See RHBDL3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RHBDL3

    SOURCE GeneReport for Unigene cluster: Hs.655027
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for RHBDL3 gene from 6/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rhbdl31 , 5 rhomboid, veinlet-like 3 (Drosophila)1, 5 90.59(n)1
    95.54(a)1
      11 (47.73 cM)5
    2461041  NM_139228.31  NP_631974.11 
     803009125 
    chicken
    (Gallus gallus)
    Aves RHBDL31 rhomboid, veinlet-like 3 (Drosophila) 78.14(n)
    87.7(a)
      417411  XM_415663.2  XP_415663.2 
    lizard
    (Anolis carolinensis)
    Reptilia RHBDL36
    rhomboid, veinlet-like 3 (Drosophila)
    86(a)
    1 ↔ 1
    GL343198.1(1716909-1796159)
    zebrafish
    (Danio rerio)
    Actinopterygii wufb98c112 Transcribed sequence with weak similarity to protein more 75.49(n)    AL726021.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta stet1 stem cell tumor 52.2(n)
    43.97(a)
      38169  NM_176272.1  NP_788450.1 
    worm
    (Caenorhabditis elegans)
    Secernentea rom-16
    rom-26
    Rhomboid-related protein 2
    25(a)
    15(a)
    many ↔ many
    many ↔ many
    III(4907226-4908822)
    III(9592282-9595574)


    ENSEMBL Gene Tree for RHBDL3 (if available)
    TreeFam Gene Tree for RHBDL3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RHBDL3 gene
    RHBDL22  RHBDL12  
    2 SIMAP similar genes for RHBDL3 using alignment to 5 protein entries:     RHBL3_HUMAN (see all proteins):
    RHBDL1    RHBDL2

    RHBDL3 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

    10/1356 SNPs in RHBDL3 are shown (see all 1356)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1885330981,2
    --30591199(+) AATACA/GTGTTC 1 -- us2k10--------
    rs580997561,2
    C--30591266(+) ATATG-/TTGATA 1 -- us2k10--------
    rs360967671,2
    C--30591306(+) CTCCCA/-TGGGT 1 -- us2k12Minor allele frequency- -:0.25NA CSA 4
    rs664943491,2
    C--30591307(+) TCCCT-/AGGGTA 1 -- us2k10--------
    rs99150421,2
    C,F,A,H--30591380(+) GTGCCC/TTTCTC 1 -- us2k1 trp311Minor allele frequency- T:0.36NA WA CSA EA 374
    rs1426525111,2
    --30591476(+) TCATGC/TAAATG 1 -- us2k10--------
    rs571719381,2
    C,F--30591524(+) GGGCCC/GCAGCG 1 -- us2k11Minor allele frequency- G:0.13WA 118
    rs124513381,2
    C,F,H--30591529(+) CCAGCA/GGTCAT 1 -- us2k114Minor allele frequency- G:0.49NA WA CSA EA 378
    rs1179782141,2
    C,F--30591706(+) AAATAG/ATTGAA 1 -- us2k11Minor allele frequency- A:0.02EA 120
    rs769898701,2
    C,F--30591764(+) ACTCAC/ACTAAT 1 -- us2k11Minor allele frequency- A:0.03EA 120

    HapMap Linkage Disequilibrium report for RHBDL3 (30593195 - 30651680 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for RHBDL3:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2715834CNV Deletion23290073
    esv1001216CNV Deletion20482838
    esv2238058CNV Deletion18987734
    esv2715835CNV Deletion23290073
    esv2672269CNV Deletion23128226
    esv2621296CNV Insertion19546169
    nsv908068CNV Gain21882294
    nsv827949CNV Gain20364138
    nsv908069CNV Gain21882294
    esv29073CNV Gain19812545

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing RHBDL3
    DNA2.0 Custom Variant and Variant Library Synthesis for RHBDL3

    (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
      --

    (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 RHBDL3 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with RHBDL3)
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    1. Cloning and expression of Ventrhoid, a novel vertebrate homologue of the Drosophila EGF pathway gene Rhomboid. (PubMed id 11900977)1, 2, 3 Jaszai J. and Brand M. (2002)
    2. 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. (2004)
    3. Ubiquitin-dependent intramembrane rhomboid protease pr omotes ERAD of membrane proteins. (PubMed id 22795130)1 Fleig L....Lemberg M.K. (2012)
    4. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)2 Zody M.C.... Nusbaum C. (2006)
    5. 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. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 162494 HGNC: 16502 AceView: RHBDL4 Ensembl:ENSG00000141314 euGenes: HUgn162494
    ECgene: RHBDL3 H-InvDB: RHBDL3

    (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 RHBDL3 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 RHBDL3 gene:
    Search GeneIP for patents involving RHBDL3

    GeneCards and IP:
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