Human Gene COMMD5 (uc003zem.3) Description and Page Index
  Description: Homo sapiens COMM domain containing 5 (COMMD5), transcript variant 3, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr8:146,075,551-146,078,451 Size: 2,901 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr8:146,076,049-146,076,723 Size: 675 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:146,075,551-146,078,451)mRNA (may differ from genome)Protein (224 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: COMD5_HUMAN
DESCRIPTION: RecName: Full=COMM domain-containing protein 5; AltName: Full=Hypertension-related calcium-regulated gene protein; Short=HCaRG;
FUNCTION: Down-regulates activation of NF-kappa-B.
SUBUNIT: Interacts (via COMM domain) with COMMD1 (via COMM domain).
SUBCELLULAR LOCATION: Nucleus (By similarity).
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.
SIMILARITY: Contains 1 COMM domain.
SEQUENCE CAUTION: Sequence=AAF14877.1; Type=Frameshift; Positions=66, 84, 112, 136;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): COMMD5
CDC HuGE Published Literature: COMMD5
Positive Disease Associations: Kidney Diseases
Related Studies:
  1. Kidney Diseases
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.46 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 82.81 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -55.00131-0.420 Picture PostScript Text
3' UTR -163.60498-0.329 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017920 - COMM
IPR009886 - HCaRG

Pfam Domains:
PF07258 - COMM domain

ModBase Predicted Comparative 3D Structure on Q9GZQ3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  KJ893667 - Synthetic construct Homo sapiens clone ccsbBroadEn_03061 COMMD5 gene, encodes complete protein.
KJ893668 - Synthetic construct Homo sapiens clone ccsbBroadEn_03062 COMMD5 gene, encodes complete protein.
AK023070 - Homo sapiens cDNA FLJ13008 fis, clone NT2RP3000456.
AF113540 - Homo sapiens hypothalamus protein HT002 mRNA, complete cds.
AF290195 - Homo sapiens hypertension-related calcium-regulated gene mRNA, complete cds.
BC065729 - Homo sapiens COMM domain containing 5, mRNA (cDNA clone MGC:72046 IMAGE:6452461), complete cds.
BC002672 - Homo sapiens COMM domain containing 5, mRNA (cDNA clone MGC:3418 IMAGE:3606279), complete cds.
AK001477 - Homo sapiens cDNA FLJ10615 fis, clone NT2RP2005441.
BC003055 - Homo sapiens COMM domain containing 5, mRNA (cDNA clone MGC:947 IMAGE:3544106), complete cds.
JD059853 - Sequence 40877 from Patent EP1572962.
AK294282 - Homo sapiens cDNA FLJ57354 complete cds, highly similar to Zinc finger protein 250.
JD353518 - Sequence 334542 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9GZQ3 (Reactome details) participates in the following event(s):

R-HSA-8955289 COMMDs displace CAND1 from cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-8955285 COMMDs displace CAND1 from CRL4 E3 ubiquitin ligase complex
R-HSA-8952044 AcM-UBE2F transfers NEDD8 to CRL5 E3 ubiquitin ligase complex
R-HSA-8952618 AcM-UBE2M transfers NEDD8 to CRL1 E3 ubiquitin ligase complex
R-HSA-8952039 NEDD8:AcM-UBE2F binds CRL5 E3 ubiquitin ligase complex
R-HSA-8952620 NEDD8:AcM-UBE2M binds CRL1 E3 ubiquitin ligase complex
R-HSA-8956200 MyrG-DCUN1D3 binds CRL1 E3 ubiquitin ligase complex
R-HSA-8956099 VHL:EloB,C:NEDD8-CUL2:RBX1 complex binds UBXN7
R-HSA-8956103 VHL:EloB,C:NEDD8-CUL2:RBX1 complex binds hydroxyprolyl-HIF-alpha
R-HSA-8956045 COP9 signalosome deneddylates nuclear CRL4 E3 ubiquitin ligase complex
R-HSA-8952638 AcM-UBE2M transfers NEDD8 to CRL4 E3 ubiquitin ligase complex
R-HSA-8952639 NEDD8:AcM-UBE2M binds CRL4 E3 ubiquitin ligase complex
R-HSA-8956040 COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-8956106 VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha
R-HSA-8951664 Neddylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: COMD5_HUMAN, D3DWN7, HT002, NM_001081004, NP_054785, Q9GZQ3, Q9NVN6, Q9UHX5
UCSC ID: uc003zem.3
RefSeq Accession: NM_001081004
Protein: Q9GZQ3 (aka COMD5_HUMAN or COM5_HUMAN)
CCDS: CCDS6436.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001081004.1
exon count: 2CDS single in 3' UTR: no RNA size: 1320
ORF size: 675CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1550.00frame shift in genome: no % Coverage: 98.79
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 382# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.