Cox20 (cytochrome c oxidase assembly factor COX20) - Rat Genome Database

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Gene: Cox20 (cytochrome c oxidase assembly factor COX20) Rattus norvegicus
Analyze
Symbol: Cox20
Name: cytochrome c oxidase assembly factor COX20
RGD ID: 1309105
Description: Predicted to be involved in mitochondrial cytochrome c oxidase assembly. Predicted to be located in mitochondrial inner membrane. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in mitochondrial complex IV deficiency nuclear type 11. Orthologous to human COX20 (cytochrome c oxidase assembly factor COX20); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; aconitine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: COX20 Cox2 chaperone homolog; COX20 Cox2 chaperone homolog (S. cerevisiae); COX20 cytochrome C oxidase assembly factor; Fam36a; family with sequence similarity 36, member A; hypothetical protein LOC289278; LOC289278; RGD1309105; similar to RIKEN cDNA 2310005N03 gene; uncharacterized protein LOC289278
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81392,592,260 - 92,604,129 (+)NCBIGRCr8
mRatBN7.21390,065,900 - 90,075,386 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1392,573,162 - 92,577,332 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01393,973,304 - 93,977,474 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01391,154,900 - 91,159,068 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01396,219,853 - 96,224,023 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1396,219,853 - 96,224,023 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013100,660,978 - 100,665,148 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41393,969,033 - 93,973,203 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11394,157,910 - 94,162,394 (+)NCBI
Celera1389,626,715 - 89,630,882 (+)NCBICelera
Cytogenetic Map13q25NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18614015   PMID:23125284   PMID:24403053  


Genomics

Comparative Map Data
Cox20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81392,592,260 - 92,604,129 (+)NCBIGRCr8
mRatBN7.21390,065,900 - 90,075,386 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1392,573,162 - 92,577,332 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01393,973,304 - 93,977,474 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01391,154,900 - 91,159,068 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01396,219,853 - 96,224,023 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1396,219,853 - 96,224,023 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013100,660,978 - 100,665,148 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41393,969,033 - 93,973,203 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11394,157,910 - 94,162,394 (+)NCBI
Celera1389,626,715 - 89,630,882 (+)NCBICelera
Cytogenetic Map13q25NCBI
COX20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381244,835,306 - 244,845,063 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1244,835,616 - 244,845,057 (+)EnsemblGRCh38hg38GRCh38
GRCh371244,998,608 - 245,008,365 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361243,065,262 - 243,074,982 (+)NCBINCBI36Build 36hg18NCBI36
Build 341241,325,003 - 241,332,998NCBI
Celera1218,288,590 - 218,298,310 (+)NCBICelera
Cytogenetic Map1q44NCBI
HuRef1215,381,801 - 215,391,521 (+)NCBIHuRef
CHM1_11246,270,981 - 246,280,707 (+)NCBICHM1_1
T2T-CHM13v2.01244,251,611 - 244,261,368 (+)NCBIT2T-CHM13v2.0
Cox20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391178,146,379 - 178,150,258 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1178,146,695 - 178,150,258 (+)EnsemblGRCm39 Ensembl
GRCm381178,318,095 - 178,322,693 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1178,319,130 - 178,322,693 (+)EnsemblGRCm38mm10GRCm38
MGSCv371180,249,284 - 180,252,824 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361180,155,828 - 180,159,368 (+)NCBIMGSCv36mm8
Celera1185,378,778 - 185,382,318 (+)NCBICelera
Cytogenetic Map1H4NCBI
cM Map183.16NCBI
LOC102016346
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554067,994,226 - 8,002,639 (+)NCBIChiLan1.0ChiLan1.0
LOC100992118
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214,308,553 - 4,318,158 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan114,533,005 - 4,540,869 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01220,432,447 - 220,440,416 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11225,812,621 - 225,820,925 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1225,812,621 - 225,820,925 (+)Ensemblpanpan1.1panPan2
COX20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1735,819,647 - 35,823,983 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl735,821,040 - 35,823,862 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha735,290,661 - 35,297,709 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0735,646,109 - 35,653,119 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1735,481,577 - 35,488,625 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0735,496,612 - 35,503,662 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0735,762,159 - 35,769,209 (+)NCBIUU_Cfam_GSD_1.0
LOC101957904
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934448,649,580 - 48,716,259 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365266,031,038 - 6,032,022 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365266,031,038 - 6,063,842 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COX20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1017,471,908 - 17,477,392 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11017,471,837 - 17,477,394 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21019,937,274 - 19,942,798 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COX20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12581,861,673 - 81,869,597 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2581,862,035 - 81,869,506 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605584,086,038 - 84,096,523 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101726175
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477114,767,882 - 14,780,938 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cox20
32 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:472
Count of miRNA genes:235
Interacting mature miRNAs:275
Transcripts:ENSRNOT00000006154
Prediction methods:Microtar, Miranda, Rnahybrid
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

Markers in Region
RH129823  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,070,191 - 90,070,346 (+)MAPPERmRatBN7.2
Rnor_6.01396,222,122 - 96,222,276NCBIRnor6.0
Rnor_5.013100,663,247 - 100,663,401UniSTSRnor5.0
RGSC_v3.41393,971,302 - 93,971,456UniSTSRGSC3.4
Celera1389,628,984 - 89,629,138UniSTS
RH 3.4 Map13607.5UniSTS
Cytogenetic Map13q26UniSTS
RH131715  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,069,151 - 90,069,517 (+)MAPPERmRatBN7.2
Rnor_6.01396,221,082 - 96,221,447NCBIRnor6.0
Rnor_5.013100,662,207 - 100,662,572UniSTSRnor5.0
RGSC_v3.41393,970,262 - 93,970,627UniSTSRGSC3.4
Celera1389,627,944 - 89,628,309UniSTS
RH 3.4 Map13609.1UniSTS
Cytogenetic Map13q26UniSTS
RH132995  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,071,046 - 90,071,710 (+)MAPPERmRatBN7.2
Rnor_6.01396,222,977 - 96,223,640NCBIRnor6.0
Rnor_5.013100,664,102 - 100,664,765UniSTSRnor5.0
RGSC_v3.41393,972,157 - 93,972,820UniSTSRGSC3.4
Celera1389,629,839 - 89,630,499UniSTS
RH 3.4 Map13607.7UniSTS
Cytogenetic Map13q26UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000006154   ⟹   ENSRNOP00000006154
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1396,219,853 - 96,224,023 (+)Ensembl
RefSeq Acc Id: NM_001105976   ⟹   NP_001099446
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81392,599,959 - 92,604,129 (+)NCBI
mRatBN7.21390,067,923 - 90,072,093 (+)NCBI
Rnor_6.01396,219,853 - 96,224,023 (+)NCBI
Rnor_5.013100,660,978 - 100,665,148 (+)NCBI
RGSC_v3.41393,969,033 - 93,973,203 (+)RGD
Celera1389,626,715 - 89,630,882 (+)RGD
Sequence:
RefSeq Acc Id: XM_039090533   ⟹   XP_038946461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81392,592,260 - 92,603,783 (+)NCBI
mRatBN7.21390,065,900 - 90,075,386 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001099446 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946461 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94799 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000081441.1
RefSeq Acc Id: NP_001099446   ⟸   NM_001105976
- UniProtKB: A6JGE3 (UniProtKB/TrEMBL),   A0A8I5ZSY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006154   ⟸   ENSRNOT00000006154
RefSeq Acc Id: XP_038946461   ⟸   XM_039090533
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYU4-F1-model_v2 AlphaFold D3ZYU4 1-117 view protein structure

Transcriptome

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

Promoters
RGD ID:13699049
Promoter ID:EPDNEW_R9573
Type:multiple initiation site
Name:Cox20_1
Description:COX20 cytochrome C oxidase assembly factor
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_6.01396,220,092 - 96,220,152EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309105 AgrOrtholog
BioCyc Gene G2FUF-17174 BioCyc
Ensembl Genes ENSRNOG00000004553 Ensembl
  ENSRNOG00000050982 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074231.4 UniProtKB/TrEMBL
InterPro Cox20 UniProtKB/TrEMBL
KEGG Report rno:289278 UniProtKB/TrEMBL
NCBI Gene 289278 ENTREZGENE
PANTHER CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX20, MITOCHONDRIAL UniProtKB/TrEMBL
  CYTOCHROME C OXIDASE PROTEIN 20 UniProtKB/TrEMBL
Pfam Cox20 UniProtKB/TrEMBL
PhenoGen Cox20 PhenoGen
PRINTS PROTEINF36A UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004553 RatGTEx
  ENSRNOG00000050982 RatGTEx
UniProt A0A8I5ZSY5 ENTREZGENE, UniProtKB/TrEMBL
  A6JGE3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-07-20 Cox20  cytochrome c oxidase assembly factor COX20  Cox20  COX20 cytochrome C oxidase assembly factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-06-05 Cox20  COX20 cytochrome C oxidase assembly factor  Cox20  COX20 Cox2 chaperone homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-16 Cox20  COX20 Cox2 chaperone homolog (S. cerevisiae)  Fam36a  family with sequence similarity 36, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Fam36a  family with sequence similarity 36, member A  RGD1309105_predicted  similar to RIKEN cDNA 2310005N03 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 RGD1309105_predicted  similar to RIKEN cDNA 2310005N03 gene  Fam36a_predicted  family with sequence similarity 36, member A (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Fam36a_predicted  family with sequence similarity 36, member A (predicted)      Symbol and Name status set to approved 70820 APPROVED