Cog4 (component of oligomeric golgi complex 4) - Rat Genome Database

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Gene: Cog4 (component of oligomeric golgi complex 4) Rattus norvegicus
Analyze
Symbol: Cog4
Name: component of oligomeric golgi complex 4
RGD ID: 1310549
Description: Predicted to enable identical protein binding activity. Predicted to be involved in Golgi organization; Golgi vesicle transport; and glycosylation. Predicted to be located in membrane. Predicted to be part of Golgi transport complex. Human ortholog(s) of this gene implicated in Saul-Wilson syndrome and congenital disorder of glycosylation type IIj. Orthologous to human COG4 (component of oligomeric golgi complex 4); INTERACTS WITH 3-chloropropane-1,2-diol; 4,4'-sulfonyldiphenol; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: conserved oligomeric Golgi complex subunit 4; LOC361407
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81955,729,854 - 55,763,902 (+)NCBIGRCr8
mRatBN7.21938,820,478 - 38,854,803 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1938,820,501 - 38,854,796 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1945,625,539 - 45,658,998 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01946,278,907 - 46,312,366 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01948,589,673 - 48,623,318 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01943,358,057 - 43,391,828 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1943,358,057 - 43,391,828 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01954,191,116 - 54,224,687 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41940,769,219 - 40,803,409 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11940,774,043 - 40,808,258 (+)NCBI
Celera1938,214,041 - 38,247,592 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15047703   PMID:19536132   PMID:19651599  


Genomics

Comparative Map Data
Cog4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81955,729,854 - 55,763,902 (+)NCBIGRCr8
mRatBN7.21938,820,478 - 38,854,803 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1938,820,501 - 38,854,796 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1945,625,539 - 45,658,998 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01946,278,907 - 46,312,366 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01948,589,673 - 48,623,318 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01943,358,057 - 43,391,828 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1943,358,057 - 43,391,828 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01954,191,116 - 54,224,687 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41940,769,219 - 40,803,409 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11940,774,043 - 40,808,258 (+)NCBI
Celera1938,214,041 - 38,247,592 (+)NCBICelera
Cytogenetic Map19q12NCBI
COG4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381670,480,567 - 70,523,554 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1670,480,568 - 70,523,560 (-)EnsemblGRCh38hg38GRCh38
GRCh371670,514,470 - 70,557,457 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361669,071,973 - 69,114,958 (-)NCBINCBI36Build 36hg18NCBI36
Build 341669,071,977 - 69,114,935NCBI
Celera1654,970,686 - 55,013,821 (+)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1656,346,588 - 56,388,520 (-)NCBIHuRef
CHM1_11671,921,846 - 71,964,791 (-)NCBICHM1_1
T2T-CHM13v2.01676,291,598 - 76,334,735 (-)NCBIT2T-CHM13v2.0
Cog4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398111,573,232 - 111,608,866 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8111,573,232 - 111,608,859 (+)EnsemblGRCm39 Ensembl
GRCm388110,846,600 - 110,882,234 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8110,846,600 - 110,882,227 (+)EnsemblGRCm38mm10GRCm38
MGSCv378113,370,924 - 113,406,134 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368113,733,724 - 113,768,902 (+)NCBIMGSCv36mm8
Celera8115,070,562 - 115,105,856 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map857.76NCBI
Cog4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554843,279,302 - 3,307,543 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554843,278,624 - 3,307,580 (-)NCBIChiLan1.0ChiLan1.0
COG4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21883,639,783 - 83,682,396 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11689,569,110 - 89,611,773 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01654,491,189 - 54,533,770 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11670,318,788 - 70,360,843 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1670,318,788 - 70,360,843 (-)Ensemblpanpan1.1panPan2
COG4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1576,463,465 - 76,490,406 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl576,463,465 - 76,490,376 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha576,424,749 - 76,451,695 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0576,899,880 - 76,926,816 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl576,899,880 - 76,926,802 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1576,721,873 - 76,748,762 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0576,544,892 - 76,571,829 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0577,036,954 - 77,064,098 (-)NCBIUU_Cfam_GSD_1.0
Cog4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934936,472,911 - 36,502,714 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647523,086,372 - 23,119,163 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647523,086,406 - 23,116,203 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COG4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl613,490,116 - 13,524,452 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1613,492,876 - 13,524,442 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
COG4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1553,635,045 - 53,673,205 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl553,635,485 - 53,673,227 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604716,431,232 - 16,471,696 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cog4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474612,715,437 - 12,747,823 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474612,715,437 - 12,747,187 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cog4
159 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:187
Count of miRNA genes:140
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000023927
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
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat

Markers in Region
AW531097  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21938,840,737 - 38,840,937 (-)MAPPERmRatBN7.2
Rnor_6.01943,371,397 - 43,371,596NCBIRnor6.0
Rnor_5.01954,204,486 - 54,204,685UniSTSRnor5.0
RGSC_v3.41940,789,840 - 40,790,039UniSTSRGSC3.4
Celera1938,234,337 - 38,234,536UniSTS
RH 3.4 Map19475.7UniSTS
Cytogenetic Map19q12UniSTS
AW535207  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21938,825,182 - 38,825,384 (-)MAPPERmRatBN7.2
Rnor_6.01943,386,949 - 43,387,150NCBIRnor6.0
Rnor_5.01954,219,882 - 54,220,083UniSTSRnor5.0
RGSC_v3.41940,773,897 - 40,774,098UniSTSRGSC3.4
Celera1938,218,719 - 38,218,920UniSTS
RH 3.4 Map19471.8UniSTS
Cytogenetic Map19q12UniSTS


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: ENSRNOT00000023927   ⟹   ENSRNOP00000023924
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1938,820,501 - 38,854,796 (+)Ensembl
Rnor_6.0 Ensembl1943,358,057 - 43,391,828 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098170   ⟹   ENSRNOP00000085274
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1938,820,501 - 38,854,796 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099948   ⟹   ENSRNOP00000086236
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1938,820,514 - 38,854,529 (+)Ensembl
RefSeq Acc Id: NM_001108449   ⟹   NP_001101919
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,729,878 - 55,763,902 (+)NCBI
mRatBN7.21938,820,505 - 38,854,531 (+)NCBI
Rnor_6.01943,358,057 - 43,391,828 (-)NCBI
Rnor_5.01954,191,116 - 54,224,687 (-)NCBI
RGSC_v3.41940,769,219 - 40,803,409 (+)RGD
Celera1938,214,041 - 38,247,592 (+)RGD
Sequence:
RefSeq Acc Id: XM_039097859   ⟹   XP_038953787
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,735,326 - 55,763,886 (+)NCBI
mRatBN7.21938,825,807 - 38,854,803 (+)NCBI
RefSeq Acc Id: XM_063278137   ⟹   XP_063134207
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,732,905 - 55,763,886 (+)NCBI
RefSeq Acc Id: XM_063278138   ⟹   XP_063134208
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,729,854 - 55,750,332 (+)NCBI
RefSeq Acc Id: NP_001101919   ⟸   NM_001108449
- UniProtKB: D3ZZM3 (UniProtKB/TrEMBL),   A6IZ72 (UniProtKB/TrEMBL),   A0A8I6A3P8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023924   ⟸   ENSRNOT00000023927
RefSeq Acc Id: XP_038953787   ⟸   XM_039097859
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000086236   ⟸   ENSRNOT00000099948
RefSeq Acc Id: ENSRNOP00000085274   ⟸   ENSRNOT00000098170
RefSeq Acc Id: XP_063134208   ⟸   XM_063278138
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063134207   ⟸   XM_063278137
- Peptide Label: isoform X1
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZM3-F1-model_v2 AlphaFold D3ZZM3 1-785 view protein structure

Transcriptome

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

Promoters
RGD ID:13701145
Promoter ID:EPDNEW_R11669
Type:multiple initiation site
Name:Cog4_1
Description:component of oligomeric golgi complex 4
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_6.01943,391,823 - 43,391,883EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310549 AgrOrtholog
BioCyc Gene G2FUF-5675 BioCyc
Ensembl Genes ENSRNOG00000017745 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023927 ENTREZGENE
  ENSRNOT00000023927.6 UniProtKB/TrEMBL
  ENSRNOT00000098170.1 UniProtKB/TrEMBL
  ENSRNOT00000099948.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.1970 UniProtKB/TrEMBL
  ESAT-6-like UniProtKB/TrEMBL
InterPro COG4 UniProtKB/TrEMBL
  COG4 UniProtKB/TrEMBL
  COG4_C UniProtKB/TrEMBL
  COG4_N UniProtKB/TrEMBL
KEGG Report rno:361407 UniProtKB/TrEMBL
NCBI Gene 361407 ENTREZGENE
PANTHER CONSERVED OLIGOMERIC GOLGI COMPLEX SUBUNIT 4 UniProtKB/TrEMBL
  CONSERVED OLIGOMERIC GOLGI COMPLEX SUBUNIT 4 UniProtKB/TrEMBL
Pfam COG4 UniProtKB/TrEMBL
  COG4_C UniProtKB/TrEMBL
  COG4_N UniProtKB/TrEMBL
PhenoGen Cog4 PhenoGen
RatGTEx ENSRNOG00000017745 RatGTEx
SMART Cog4 UniProtKB/TrEMBL
UniProt A0A8I6A3P8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A5F9_RAT UniProtKB/TrEMBL
  A6IZ72 ENTREZGENE, UniProtKB/TrEMBL
  D3ZZM3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Cog4  component of oligomeric golgi complex 4   Cog4_predicted  component of oligomeric golgi complex 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cog4_predicted  component of oligomeric golgi complex 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED