Commd3 (COMM domain containing 3) - Rat Genome Database

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Gene: Commd3 (COMM domain containing 3) Rattus norvegicus
Analyze
Symbol: Commd3
Name: COMM domain containing 3
RGD ID: 735116
Description: Predicted to be involved in sodium ion transport. Predicted to be located in cytoplasm and nucleus. Orthologous to human COMMD3 (COMM domain containing 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: COMM domain-containing protein 3; MGC72959; Unknown (protein for MGC:72959)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81786,235,863 - 86,239,610 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1786,235,863 - 86,239,610 (+)EnsemblGRCr8
mRatBN7.21781,327,444 - 81,331,191 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1781,327,405 - 81,331,177 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1784,800,687 - 84,804,431 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01788,636,087 - 88,639,831 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01782,652,829 - 82,656,573 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01785,356,042 - 85,359,835 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1785,356,042 - 85,359,833 (+)Ensemblrn6Rnor6.0
Rnor_5.01787,079,392 - 87,083,185 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41792,775,474 - 92,779,187 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1780,609,621 - 80,611,929 (+)NCBICelera
RGSC_v3.11792,786,306 - 92,790,020 (+)NCBI
Cytogenetic Map17q12.3NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-acetamidofluorene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-lapachone  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
carbamazepine  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dicrotophos  (ISO)
diethyl maleate  (ISO)
dimethyl sulfoxide  (ISO)
elemental selenium  (ISO)
finasteride  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
inulin  (ISO)
ivermectin  (ISO)
methylparaben  (ISO)
mitomycin C  (ISO)
N-nitrosodiethylamine  (ISO)
nickel sulfate  (ISO)
nitrates  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (EXP)
piperonyl butoxide  (ISO)
potassium chromate  (ISO)
resveratrol  (ISO)
selenium atom  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulfadimethoxine  (EXP)
sulindac  (EXP)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:23637203  


Genomics

Comparative Map Data
Commd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81786,235,863 - 86,239,610 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1786,235,863 - 86,239,610 (+)EnsemblGRCr8
mRatBN7.21781,327,444 - 81,331,191 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1781,327,405 - 81,331,177 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1784,800,687 - 84,804,431 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01788,636,087 - 88,639,831 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01782,652,829 - 82,656,573 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01785,356,042 - 85,359,835 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1785,356,042 - 85,359,833 (+)Ensemblrn6Rnor6.0
Rnor_5.01787,079,392 - 87,083,185 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41792,775,474 - 92,779,187 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1780,609,621 - 80,611,929 (+)NCBICelera
RGSC_v3.11792,786,306 - 92,790,020 (+)NCBI
Cytogenetic Map17q12.3NCBI
COMMD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381022,316,388 - 22,320,306 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1022,315,980 - 22,320,430 (+)Ensemblhg38GRCh38
GRCh371022,605,317 - 22,609,235 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361022,645,305 - 22,649,243 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341022,645,304 - 22,649,243NCBI
Celera1022,293,008 - 22,296,946 (+)NCBICelera
Cytogenetic Map10p12.2NCBI
HuRef1022,266,781 - 22,270,715 (+)NCBIHuRef
CHM1_11022,606,039 - 22,609,973 (+)NCBICHM1_1
T2T-CHM13v2.01022,335,422 - 22,339,340 (+)NCBIT2T-CHM13v2.0
Commd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39218,677,246 - 18,681,042 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl218,677,234 - 18,681,042 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38218,672,435 - 18,676,231 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl218,672,384 - 18,676,231 (+)Ensemblmm10GRCm38
MGSCv37218,594,089 - 18,597,843 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36218,590,216 - 18,593,970 (+)NCBIMGSCv36mm8
Celera218,564,347 - 18,568,097 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map212.9NCBI
Commd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554296,559,719 - 6,564,414 (-)Ensembl
ChiLan1.0NW_0049554296,559,824 - 6,563,701 (-)NCBIChiLan1.0ChiLan1.0
COMMD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2834,996,486 - 35,000,478 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11035,001,811 - 35,005,803 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01022,473,001 - 22,476,953 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11022,848,417 - 22,852,396 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1022,848,417 - 22,852,396 (+)EnsemblpanPan2panpan1.1
COMMD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1210,829,693 - 10,833,643 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl210,818,232 - 10,833,613 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha29,523,153 - 9,527,025 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.029,029,718 - 9,033,594 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl29,018,100 - 9,033,607 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.128,393,400 - 8,397,270 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.028,477,575 - 8,481,443 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.028,645,450 - 8,649,327 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Commd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934422,237,251 - 22,241,696 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365205,718,150 - 5,723,257 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365205,718,776 - 5,722,644 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COMMD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1052,597,587 - 52,601,733 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11052,597,391 - 52,601,376 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21058,251,896 - 58,255,880 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COMMD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1922,090,426 - 22,094,386 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605127,833,050 - 27,837,814 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Commd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247966,287,849 - 6,291,671 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247966,288,057 - 6,291,618 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Commd3
20 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:36
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000022201
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300131Bp193Blood pressure QTL 1933.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176855004093515804Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)174238816487388164Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174238816487388164Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)174605012691050126Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175819406487388164Rat
61466Niddm12Non-insulin dependent diabetes mellitus QTL 123.20.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)176515487293515804Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175560459793006569Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175482950393515804Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)176456982086954580Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)174265489587654895Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174096801789341781Rat

Markers in Region
D17Rat154  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81786,201,128 - 86,201,342 (+)Marker Load Pipeline
mRatBN7.21781,292,711 - 81,292,925 (+)MAPPERmRatBN7.2
Rnor_6.01785,321,344 - 85,321,557NCBIRnor6.0
Rnor_5.01787,044,959 - 87,045,172UniSTSRnor5.0
RGSC_v3.41792,741,004 - 92,741,217RGDRGSC3.4
RGSC_v3.41792,741,005 - 92,741,218UniSTSRGSC3.4
Celera1780,573,375 - 80,573,588UniSTS
RGSC_v3.11792,751,837 - 92,752,050RGD
SHRSP x BN Map1747.5999UniSTS
SHRSP x BN Map1747.5999RGD
Cytogenetic Map17q12.3UniSTS
RH144129  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21781,328,405 - 81,328,643 (+)MAPPERmRatBN7.2
Rnor_6.01785,357,061 - 85,357,298NCBIRnor6.0
Rnor_5.01787,080,411 - 87,080,648UniSTSRnor5.0
RGSC_v3.41792,776,413 - 92,776,650UniSTSRGSC3.4
Celera1780,609,155 - 80,609,392UniSTS
RH 3.4 Map17833.5UniSTS
Cytogenetic Map17q12.3UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000022201   ⟹   ENSRNOP00000022201
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1786,235,863 - 86,239,610 (+)Ensembl
mRatBN7.2 Ensembl1781,327,405 - 81,331,177 (+)Ensembl
Rnor_6.0 Ensembl1785,356,042 - 85,359,833 (+)Ensembl
RefSeq Acc Id: NM_198732   ⟹   NP_942027
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81786,235,863 - 86,239,610 (+)NCBI
mRatBN7.21781,327,444 - 81,331,191 (+)NCBI
Rnor_6.01785,356,042 - 85,359,835 (+)NCBI
Rnor_5.01787,079,392 - 87,083,185 (+)NCBI
RGSC_v3.41792,775,474 - 92,779,187 (+)RGD
Celera1780,609,621 - 80,611,929 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_942027 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH60591 (Get FASTA)   NCBI Sequence Viewer  
  EDL78769 (Get FASTA)   NCBI Sequence Viewer  
  EDL78770 (Get FASTA)   NCBI Sequence Viewer  
  EDL78771 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022201
  ENSRNOP00000022201.5
GenBank Protein Q6P9U3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_942027   ⟸   NM_198732
- UniProtKB: Q6P9U3 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000022201   ⟸   ENSRNOT00000022201
Protein Domains
COMM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P9U3-F1-model_v2 AlphaFold Q6P9U3 1-195 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700606
Promoter ID:EPDNEW_R11129
Type:initiation region
Name:Commd3_1
Description:COMM domain containing 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01785,356,075 - 85,356,135EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735116 AgrOrtholog
BioCyc Gene G2FUF-8559 BioCyc
Ensembl Genes ENSRNOG00000016383 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022201 ENTREZGENE
  ENSRNOT00000022201.6 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6920278 IMAGE-MGC_LOAD
InterPro COMM UniProtKB/Swiss-Prot
  COMMD3 UniProtKB/Swiss-Prot
KEGG Report rno:291339 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72959 IMAGE-MGC_LOAD
NCBI Gene 291339 ENTREZGENE
PANTHER COMM DOMAIN-CONTAINING PROTEIN 3 UniProtKB/Swiss-Prot
  PTHR31159 UniProtKB/Swiss-Prot
Pfam COMM_domain UniProtKB/Swiss-Prot
  COMM_HN UniProtKB/Swiss-Prot
PhenoGen Commd3 PhenoGen
PROSITE COMM UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000016383 RatGTEx
UniProt A6JM92_RAT UniProtKB/TrEMBL
  A6JM93_RAT UniProtKB/TrEMBL
  COMD3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Commd3  COMM domain containing 3    Unknown (protein for MGC:72959)  Name updated 1299863 APPROVED
2004-09-10 Commd3  Unknown (protein for MGC:72959)  MGC72959    Symbol and Name updated 1299863 APPROVED