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RHBDD2 Gene

protein-coding   GIFtS: 50
GCID: GC07P075471

Rhomboid Domain Containing 2

(Previous names: rhomboid, veinlet-like 7 (Drosophila))
(Previous symbol: RHBDL7)
  Search for RHBDD2
at  

(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Rhomboid Domain Containing 21 2     NPD0072
RHBDL71 2 3     WUGSC:H_RG122E10.2a2
Rhomboid, Veinlet-Like 7 (Drosophila)1     WUGSC:H_RG122E10.2b2
H_RG122E10.2a2     Rhomboid Domain-Containing Protein 22
H_RG122E10.2b2     Rhomboid, Veinlet-Like 72

External Ids:    HGNC: 230821   Entrez Gene: 574142   Ensembl: ENSG000000054867   OMIM: 6152035   UniProtKB: Q6NTF93   
ORGUL members:         

Export aliases for RHBDD2 gene to outside databases

Previous GC identifers: GC07P075346 GC07P070594


(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 RHBDD2 Gene:
RHBDD2 (rhomboid domain containing 2) 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_000007.13  NT_007933.16  NC_018918.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RHBDD2 gene promoter:
         GATA-3   Sp1   SREBP-1c   MIF-1   LCR-F1   SREBP-1b   C/EBPalpha   GATA-1   GATA-2   SREBP-1a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RHBDD2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RHBDD2


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

Entrez Gene cytogenetic band: 7q11.23   Ensembl cytogenetic band:  7q11.23   HGNC cytogenetic band: 7q11

RHBDD2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RHBDD2 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P075471:  view genomic region     (about GC identifiers)

Start:
75,471,920 bp from pter      End:
75,518,244 bp from pter
Size:
46,325 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 74,841,381-74,851,308     

(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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RHBD2_HUMAN, Q6NTF9 (See protein sequence)
Recommended Name: Rhomboid domain-containing protein 2  
Size: 364 amino acids; 39202 Da
Caution: Although strongly related to the peptidase S54 family, it lacks the conserved active sites, suggesting
that it has no peptidase activity
Sequence caution: Sequence=BAB15503.1; Type=Erroneous initiation;
Secondary accessions: Q7L534 Q9H5W6 Q9UDT2

Explore the universe of human proteins at neXtProt for RHBDD2: NX_Q6NTF9

Explore proteomics data for RHBDD2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys51, Lys230
  • Modification sites at PhosphoSitePlus

  • See RHBDD2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001035546.1  NP_001035547.1  

    ENSEMBL proteins: 
     ENSP00000006777   ENSP00000403507   ENSP00000391232   ENSP00000314144  

    RHBDD2 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for RHBDD2

     
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    Cloud-Clone Corp. ELISAs for RHBDD2
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    Search eBioscience for ELISAs for RHBDD2 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR022764 Peptidase_S54_rhomboid_dom

    Graphical View of Domain Structure for InterPro Entry Q6NTF9

    ProtoNet protein and cluster: Q6NTF9

    1 Blocks protein domain: IPB002610 Rhomboid-like protein

    UniProtKB/Swiss-Prot: RHBD2_HUMAN, Q6NTF9
    Similarity: Belongs to the peptidase S54 family


    Find genes that share domains with RHBDD2           About GenesLikeMe


    (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,
    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:0004252serine-type endopeptidase activity IEA--
         
    Find genes that share ontologies with RHBDD2           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RHBDD2
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    miRNA
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    miRTarBase miRNAs that target RHBDD2:
    hsa-let-7e-5p (MIRT051463)

    Block miRNA regulation of human, mouse, rat RHBDD2 using miScript Target Protectors
    5 qRT-PCR Assays for microRNAs that regulate RHBDD2:
    hsa-miR-221* hsa-miR-520d-5p hsa-miR-544 hsa-miR-524-5p hsa-let-7f-2*
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat RHBDD2

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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
    RHBD2_HUMAN, Q6NTF9: Golgi apparatus, cis-Golgi network membrane; Multi-pass membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    golgi apparatus4
    nucleus4
    plasma membrane3

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005794Golgi apparatus IDA--
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with RHBDD2           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 RHBDD2
    Interactions:

        Search GeneGlobe Interaction Network for RHBDD2

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

    4 Interacting proteins for RHBDD2 (Q6NTF93 ENSP000000067774) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BECN1Q144573I2D: score=1 
    CAMKK2Q96RR43I2D: score=1 
    CLN3Q132863I2D: score=1 
    UBCENSP000003448184STRING: 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 RHBDD2 (RHBD2)



    (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 RHBDD2 gene (3 alternative transcripts): 
    NM_020684.2  NM_001040456.1  NM_001040457.1  

    Unigene Cluster for RHBDD2:

    Rhomboid domain containing 2
    Hs.488827  [show with all ESTs]
    Unigene Representative Sequence: NM_001040457
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000466232 ENST00000468644 ENST00000006777 ENST00000454791 ENST00000476218
    ENST00000468304 ENST00000428119 ENST00000467406 ENST00000318622(uc003udv.1 uc003udw.1)

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat RHBDD2 using miScript Target Protectors
    5 qRT-PCR Assays for microRNAs that regulate RHBDD2:
    hsa-miR-221* hsa-miR-520d-5p hsa-miR-544 hsa-miR-524-5p hsa-let-7f-2*
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat RHBDD2
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      QuantiTect SYBR Green Assays in human, mouse, rat RHBDD2
      QuantiFast Probe-based Assays in human, mouse, rat RHBDD2

    Additional mRNA sequence: 

    AF226732.1 AK026590.1 BC006234.2 BC069017.1 

    18 DOTS entries:

    DT.100712002  DT.448851  DT.100037815  DT.121078101  DT.91760918  DT.100821667  DT.101984259  DT.40107293 
    DT.121078092  DT.95276407  DT.100037814  DT.100821668  DT.121078077  DT.97810745  DT.97848535  DT.100821675 
    DT.100821677  DT.91728492 

    Selected AceView cDNA sequences (see all 534):

    BG469644 BQ024997 CA312734 BI820224 CF454916 CR613112 BQ436499 AA078592 
    CR600296 AI262602 BX282531 AL519514 BM805478 AA843927 BU159178 CN480926 
    AA477522 BX463711 BM688453 BP351279 BG748384 BG110984 CD671975 BI820658 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for RHBDD2 (see all 8)    About this scheme

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


    ECgene alternative splicing isoforms for RHBDD2

    (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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    RHBDD2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGTCTGCCT
    RHBDD2 Expression
    About this image


    RHBDD2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)
             Cerebral Cortex
     
     Lung (Respiratory System)
     
     Thyroid (Endocrine System)
     
     Testis (Reproductive System)
     
     Adrenal Gland (Endocrine System)
    RHBDD2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RHBDD2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.488827
        Custom PCR Arrays for RHBDD2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RHBDD2

    (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 RHBDD2 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rhbdd21 , 5 rhomboid domain containing 21, 5 85.69(n)1
    88.09(a)1
      5 (75.31 cM)5
    2151601  NM_146002.21  NP_666114.11 
     1356326185 
    chicken
    (Gallus gallus)
    Aves RHBDD21 rhomboid domain containing 2 62.96(n)
    56.25(a)
      417521  XM_415769.4  XP_415769.4 
    lizard
    (Anolis carolinensis)
    Reptilia RHBDD26
    rhomboid domain containing 2
    44(a)
    1 ↔ 1
    GL343734.1(209757-214661)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia rhbdd21 rhomboid domain containing 2 50.39(n)
    41.8(a)
      448627  NM_001006861.1  NP_001006862.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rhbdd26
    rhomboid domain containing 2
    23(a)
    1 ↔ 1
    10(36338002-36345063) ENSDARG00000092463


    ENSEMBL Gene Tree for RHBDD2 (if available)
    TreeFam Gene Tree for RHBDD2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RHBDD2 gene
    2 SIMAP similar genes for RHBDD2 using alignment to 1 protein entry:     RHBD2_HUMAN:
    RHBDL7    WUGSC

    Find genes that share paralogs with RHBDD2           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 RHBDD2 (see all 306)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1379692631,2
    --75506350(+) CAGGAA/GCTTCT 2 -- us2k10--------
    rs1856659241,2
    --75506486(+) AGTACC/TGGGCA 2 -- us2k10--------
    rs1490905551,2
    --75506627(+) GCCTGA/GCCAAT 2 -- us2k10--------
    rs1893135421,2
    --75506857(+) CTGTTA/CTCCAG 2 -- us2k10--------
    rs1816847191,2
    --75506884(+) ACTGTA/GAAGTG 2 -- us2k10--------
    rs102330771,2
    C,F,A--75507122(+) ACAGGC/AACGCG 2 -- us2k16Minor allele frequency- A:0.50NA WA CSA 10
    rs1388065401,2
    C--75507146(+) TTAATG/TTTTGT 2 -- us2k10--------
    rs1857184801,2
    C--75507153(+) TTGTAC/GTTTTA 2 -- us2k10--------
    rs793133861,2
    C--75507278(+) GCCTCC/TTGCCC 2 -- us2k12Minor allele frequency- T:0.19NA 122
    rs1885653551,2
    --75507438(+) TAGGGA/TTGAAT 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for RHBDD2 (75471920 - 75518244 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RHBDD2:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv120n16CNV Deletion17901297
    nsv528969CNV Gain19592680
    essv14753CNV CNV17122850

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing RHBDD2
    DNA2.0 Custom Variant and Variant Library Synthesis for RHBDD2

    (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: 615203    OMIM disorders: --


    Find genes that share disorders with RHBDD2           About GenesLikeMe


    Export disorders for RHBDD2 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 RHBDD2 gene, integrated from 10 sources (see all 18):
    (articles sorted by number of sources associating them with RHBDD2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Dynamics of the rhomboid-like protein RHBDD2 expression in mouse retina and involvement of its human ortholog in retinitis pigmentosa. (PubMed id 23386608)1, 2 Ahmedli N.B....Farber D.B. (J. Biol. Chem. 2013)
    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. (Genome Res. 2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Human and mouse proteases: a comparative genomic approach. (PubMed id 12838346)1, 3 Puente X.S.... Lopez-Otin C. (Nat. Rev. Genet. 2003)
    5. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (Nature 2003)
    6. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    7. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (Sci Signal 2012)
    8. RHBDD2: a 5-fluorouracil responsive gene overexpressed in the advanced stages of colorectal cancer. (PubMed id 22965880)1 Lacunza E....Abba M.C. (Tumour Biol. 2012)
    9. 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)
    10. 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)

    (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)
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    Entrez Gene: 57414 HGNC: 23082 AceView: RHBDL7 Ensembl:ENSG00000005486 euGenes: HUgn57414
    ECgene: RHBDD2 H-InvDB: RHBDD2

    (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 RHBDD2 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 RHBDD2 gene:
    Search GeneIP for patents involving RHBDD2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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