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COMMD5 Gene

protein-coding   GIFtS: 45
GCID: GC08M146067

COMM Domain Containing 5

  See related diseases
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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Aliases
COMM Domain Containing 51 2
Hypertension-Related Calcium-Regulated Gene Protein2 3
HCARG2 5
COMM Domain-Containing Protein 52
HCaRG3

External Ids:    HGNC: 179021   Entrez Gene: 289912   Ensembl: ENSG000001706197   OMIM: 6082165   UniProtKB: Q9GZQ33   

Export aliases for COMMD5 gene to outside databases

Previous GC identifers: GC08M146069 GC08M146035 GC08M146075 GC08M141191


(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 COMMD5 Gene:
COMMD5 (COMM domain containing 5) is a protein-coding gene. Diseases associated with COMMD5 include hypertension, and diabetes mellitus.

UniProtKB/Swiss-Prot: COMD5_HUMAN, Q9GZQ3
Function: Down-regulates activation of NF-kappa-B




(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:
NC_000008.11  NT_008046.17  NC_018919.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COMMD5 gene promoter:
         AhR   AML1a   p300   AP-4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOMMD5 promoter sequence
   Search Chromatin IP Primers for COMMD5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COMMD5


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

Entrez Gene cytogenetic band: 8q24.3   Ensembl cytogenetic band:  8q24.3   HGNC cytogenetic band: 8q24.3

COMMD5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COMMD5 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M146067:  view genomic region     (about GC identifiers)

Start:
146,066,427 bp from pter      End:
146,079,121 bp from pter
Size:
12,695 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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: COMD5_HUMAN, Q9GZQ3 (See protein sequence)
Recommended Name: COMM domain-containing protein 5  
Size: 224 amino acids; 24670 Da
Subunit: Interacts (via COMM domain) with COMMD1 (via COMM domain)
Sequence caution: Sequence=AAF14877.1; Type=Frameshift; Positions=66, 84, 112, 136;
Secondary accessions: D3DWN7 Q9NVN6 Q9UHX5

Explore the universe of human proteins at neXtProt for COMMD5: NX_Q9GZQ3

Explore proteomics data for COMMD5 at MOPED


See COMMD5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (4 alternative transcripts): 
NP_001074472.1  NP_001074473.1  NP_001274166.1  NP_054785.2  

ENSEMBL proteins: 
 ENSP00000436382   ENSP00000385793   ENSP00000394331   ENSP00000304544   ENSP00000435552  
 ENSP00000433758  

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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:
 IPR017920 COMM
 IPR009886 HCaRG

Graphical View of Domain Structure for InterPro Entry Q9GZQ3

ProtoNet protein and cluster: Q9GZQ3

1 Blocks protein domain: IPB009886 HCaRG

UniProtKB/Swiss-Prot: COMD5_HUMAN, Q9GZQ3
Similarity: Contains 1 COMM domain


COMMD5 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,
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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: COMD5_HUMAN, Q9GZQ3
Function: Down-regulates activation of NF-kappa-B

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding IPI15799966
     
COMMD5 for ontologies           About GeneDecksing


Animal Models:
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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
COMD5_HUMAN, Q9GZQ3: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
extracellular1
mitochondrion1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--

COMMD5 for ontologies           About GeneDecksing


(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 COMMD5
Interactions:

    Search GeneGlobe Interaction Network for COMMD5

STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

5 Interacting proteins for COMMD5 (Q9GZQ33 ENSP000003045444) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
COMMD1Q8N6683, ENSP000003082364I2D: score=2 STRING: ENSP00000308236
NFKB1P198383, ENSP000002265744I2D: score=1 STRING: ENSP00000226574
RELBQ012013, ENSP000002214524I2D: score=1 STRING: ENSP00000221452
RELAQ042063, ENSP000003842734I2D: score=1 STRING: ENSP00000384273
SLC2A4P146723I2D: score=1 
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(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 COMMD5 (COMD5)



(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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for COMMD5 gene (4 alternative transcripts): 
NM_001081003.2  NM_001081004.2  NM_001287237.1  NM_014066.3  

Unigene Cluster for COMMD5:

COMM domain containing 5
Hs.631856  [show with all ESTs]
Unigene Representative Sequence: AF113540
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000530332(uc003zel.1) ENST00000402718(uc003zem.3) ENST00000450361(uc003zeo.4)
ENST00000305103(uc003zen.3) ENST00000529143 ENST00000533270
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Additional mRNA sequence: 

AF113540.1 AK001477.1 BC002672.2 BC003055.1 BC065729.1 

11 DOTS entries:

DT.95173493  DT.102842582  DT.97846081  DT.120630972  DT.97846079  DT.97846082  DT.413712  DT.91871287 
DT.100819074  DT.100819077  DT.120630962 

Selected AceView cDNA sequences (see all 212):

CA865627 BM128075 CA442509 BU731691 AI424759 AW005581 CD671942 BC003055 
BI837049 NM_014066 CA865895 BU508224 BG035515 AI470273 BM013651 CA417363 
CR615841 BI752248 CD365143 AK023070 BU632763 CD671718 C01217 AI004350 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for COMMD5    About this scheme

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


ECgene alternative splicing isoforms for COMMD5

(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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COMMD5 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
COMMD5 Expression
About this image

COMMD5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

COMMD5 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.631856

UniProtKB/Swiss-Prot: COMD5_HUMAN, Q9GZQ3
Tissue specificity: Highly expressed in heart, stomach, jejunum, kidney, liver, and adrenal gland. Expression was
generally higher in adult organs than in fetal tissues, particularly in heart, kidney, and liver

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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 COMMD5 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Commd51 , 5 COMM domain containing 51, 5 79.46(n)1
79.46(a)1
  15 (36.28 cM)5
663981  NM_025536.21  NP_079812.11 
 768999105 
chicken
(Gallus gallus)
Aves COMMD51 COMM domain containing 5 59.76(n)
54.5(a)
  422376  NM_001008465.1  NP_001008465.1 
tropical clawed frog
(Xenopus tropicalis)
Amphibia Str.1382 Transcribed sequence with weak similarity to protein more 72.58(n)    BX709875.1 
zebrafish
(Danio rerio)
Actinopterygii commd51 COMM domain containing 5 54.08(n)
47.06(a)
  445159  NM_001003553.1  NP_001003553.1 


ENSEMBL Gene Tree for COMMD5 (if available)
TreeFam Gene Tree for COMMD5 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for COMMD5 gene

COMMD5 for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for COMMD5
PGOHUM00000250767


(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 COMMD5 (see all 192)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 8 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1436618631,2
--146075141(+) ACCCTA/GGTGAC 3 -- int10--------
rs12098911,2
C,F,A,H--146075165(-) AGGCTA/GGAGCC 3 -- int111Minor allele frequency- G:0.30NS NA WA CSA EA 490
rs1147625711,2
C,F--146075245(+) AAGGGC/TTCCTC 3 -- int11Minor allele frequency- T:0.03WA 118
rs762581171,2
C--146075246(+) AGGGCT/CCCTCT 3 -- int13Minor allele frequency- C:0.06CSA WA NA 240
rs12098901,2
C,F,A,H--146075286(-) CTGAGA/GGCCTT 3 -- int114Minor allele frequency- G:0.45NS EA NA WA CSA 788
rs2010087541,2
C--146075286(+) AAGGC-/C/TCTCAG 3 -- int10--------
rs27366471,2
C--146075287(-) CCTGAA/GAGCCT 3 -- int10--------
rs1178185561,2
F--146075350(+) GCTTGG/ACTGCA 3 -- int11Minor allele frequency- A:0.01NA 120
rs12098891,2
F--146075375(-) CTGACA/G/TTGCTT 3 -- int12NA 4
rs12098881,2
C,F,A--146075403(-) GGGGCC/TCAGGC 3 -- int112Minor allele frequency- T:0.48NA WA CSA EA 511

HapMap Linkage Disequilibrium report for COMMD5 (146066427 - 146079121 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for COMMD5:    About this table    
Variant IDTypeSubtypePubMed ID
nsv6450CNV Insertion18451855
nsv469809CNV Loss16826518

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing COMMD5
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(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.)
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OMIM gene information: 608216    OMIM disorders: --

2 diseases for COMMD5:    
About MalaCards
hypertension    diabetes mellitus


COMMD5 for disorders           About GeneDecksing

Genetic Association Database (GAD): COMMD5
Human Genome Epidemiology (HuGE) Navigator: COMMD5 (1 document)

Export disorders for COMMD5 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 COMMD5 gene, integrated from 10 sources (see all 13):
(articles sorted by number of sources associating them with COMMD5)
    Utopia: connect your pdf to the dynamic
world of online information

  1. HCaRG, a novel calcium-regulated gene coding for a nuclear protein, is potentially involved in the regulation of cell proliferation. (PubMed id 10918053)1, 2, 3, 9 Solban N.... Tremblay J. (J. Biol. Chem. 2000)
  2. COMMD proteins, a novel family of structural and functional homologs of MURR1. (PubMed id 15799966)1, 2, 3 Burstein E.... Duckett C.S. (J. Biol. Chem. 2005)
  3. Genome-wide linkage scans for type 2 diabetes mellitus in four ethnically diverse populations-significant evidence for linkage on chromosome 4q in African Americans: the Family Investigation of Nephropathy and Diabetes Research Group. (PubMed id 19795399)1, 4 Malhotra A....Hanson R.L. (Diabetes Metab. Res. Rev. 2009)
  4. 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)
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  6. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PubMed id 10931946)1, 2 Hu R.-M.... Chen J.-L. (Proc. Natl. Acad. Sci. U.S.A. 2000)
  7. Chromosomal mapping of HCaRG, a novel hypertension-related, calcium-regulated gene. (PubMed id 11871861)1, 9 Solban N....Tremblay J. (Folia Biol. (Praha) 2002)
  8. Rosiglitazone suppresses gastric carcinogenesis by up-regulating HCaRG expression. (PubMed id 18949406)1, 9 Chen B.L....Leung W.K. (Oncol. Rep. 2008)
  9. HCaRG accelerates tubular repair after ischemic kidney injury. (PubMed id 21921141)1 Matsuda H....Tremblay J. (J. Am. Soc. Nephrol. 2011)
  10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)

(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: 28991 HGNC: 17902 AceView: COMMD5 Ensembl:ENSG00000170619 euGenes: HUgn28991
ECgene: COMMD5 H-InvDB: COMMD5

(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 COMMD5 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 COMMD5 gene:
Search GeneIP for patents involving COMMD5

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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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 inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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