Cog5 (component of oligomeric golgi complex 5) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cog5 (component of oligomeric golgi complex 5) Rattus norvegicus
Analyze
Symbol: Cog5
Name: component of oligomeric golgi complex 5
RGD ID: 1563296
Description: Predicted to be involved in inter-Golgi cisterna vesicle-mediated transport. Predicted to localize to Golgi transport complex and nucleoplasm. Human ortholog(s) of this gene implicated in congenital disorder of glycosylation type IIi. Orthologous to human COG5 (component of oligomeric golgi complex 5); INTERACTS WITH atrazine; bisphenol A; glyphosate.
Type: protein-coding
RefSeq Status: MODEL
Also known as: conserved oligomeric Golgi complex subunit 5; LOC314030; RGD1563296; similar to component of oligomeric golgi complex 5 isoform 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2648,242,470 - 48,545,185 (+)NCBI
Rnor_6.0 Ensembl650,954,631 - 51,230,701 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0650,953,868 - 51,230,860 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0659,720,284 - 59,901,509 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4649,523,386 - 50,200,662 (+)NCBIRGSC3.4rn4RGSC3.4
Celera647,444,615 - 47,730,860 (+)NCBICelera
Cytogenetic Map6q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:9792665   PMID:11980916   PMID:15047703   PMID:19946888  


Genomics

Comparative Map Data
Cog5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2648,242,470 - 48,545,185 (+)NCBI
Rnor_6.0 Ensembl650,954,631 - 51,230,701 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0650,953,868 - 51,230,860 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0659,720,284 - 59,901,509 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4649,523,386 - 50,200,662 (+)NCBIRGSC3.4rn4RGSC3.4
Celera647,444,615 - 47,730,860 (+)NCBICelera
Cytogenetic Map6q16NCBI
COG5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7107,201,372 - 107,564,261 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl7107,201,555 - 107,564,514 (-)EnsemblGRCh38hg38GRCh38
GRCh387107,201,372 - 107,564,361 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377106,841,817 - 107,204,365 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367106,630,227 - 106,991,721 (-)NCBINCBI36hg18NCBI36
Build 347106,436,941 - 106,798,436NCBI
Celera7101,647,486 - 102,010,231 (-)NCBI
Cytogenetic Map7q22.3NCBI
HuRef7101,202,742 - 101,565,584 (-)NCBIHuRef
CHM1_17106,776,168 - 107,138,910 (-)NCBICHM1_1
CRA_TCAGchr7v27106,203,276 - 106,566,048 (-)NCBI
Cog5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391231,704,848 - 31,987,629 (+)NCBIGRCm39mm39
GRCm39 Ensembl1231,704,868 - 31,987,629 (+)Ensembl
GRCm381231,654,819 - 31,937,630 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1231,654,869 - 31,937,630 (+)EnsemblGRCm38mm10GRCm38
MGSCv371232,339,734 - 32,622,495 (+)NCBIGRCm37mm9NCBIm37
Celera1233,104,592 - 33,391,997 (+)NCBICelera
Cytogenetic Map12A3NCBI
Cog5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541011,653,058 - 11,920,718 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541011,651,587 - 11,920,866 (-)NCBIChiLan1.0ChiLan1.0
COG5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17111,905,285 - 112,267,038 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7111,934,557 - 112,266,513 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0799,180,197 - 99,543,437 (-)NCBIMhudiblu_PPA_v0panPan3
COG5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1813,039,889 - 13,338,538 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11813,039,889 - 13,338,958 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cog5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647916,554,816 - 16,855,211 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COG5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9106,990,573 - 107,273,607 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19106,993,771 - 107,273,889 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29117,856,505 - 118,030,812 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COG5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12176,120,742 - 76,485,587 (-)NCBI
ChlSab1.1 Ensembl2176,122,849 - 76,479,500 (-)Ensembl
Cog5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473922,188,504 - 22,504,616 (+)NCBI

Position Markers
D6Rat27  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera647,579,075 - 47,579,338UniSTS
RH 3.4 Map6300.5UniSTS
RH 3.4 Map6300.5RGD
RH 2.0 Map6463.4RGD
SHRSP x BN Map635.2298RGD
Cytogenetic Map6q16UniSTS
BF412679  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0651,017,876 - 51,018,056NCBIRnor6.0
Rnor_5.0659,689,220 - 59,689,400UniSTSRnor5.0
RGSC_v3.4649,659,809 - 49,659,989UniSTSRGSC3.4
Celera647,518,578 - 47,518,758UniSTS
RH 3.4 Map6321.9UniSTS
Cytogenetic Map6q16UniSTS
RH144397  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0651,012,674 - 51,012,824NCBIRnor6.0
Rnor_5.0659,684,018 - 59,684,168UniSTSRnor5.0
RGSC_v3.4649,654,725 - 49,654,876UniSTSRGSC3.4
Celera647,513,375 - 47,513,525UniSTS
RH 3.4 Map6301.8UniSTS
Cytogenetic Map6q16UniSTS
RH144560  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0651,233,775 - 51,233,947NCBIRnor6.0
Rnor_5.0659,904,424 - 59,904,596UniSTSRnor5.0
RGSC_v3.4650,203,577 - 50,203,749UniSTSRGSC3.4
Celera647,733,775 - 47,733,947UniSTS
RH 3.4 Map6300.8UniSTS
Cytogenetic Map6q16UniSTS
BF408731  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0651,220,414 - 51,220,520NCBIRnor6.0
Rnor_5.0659,891,063 - 59,891,169UniSTSRnor5.0
RGSC_v3.4650,190,216 - 50,190,322UniSTSRGSC3.4
Celera647,720,414 - 47,720,520UniSTS
RH 3.4 Map6300.5UniSTS
Cytogenetic Map6q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)63425776653855198Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63626028860606186Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63760898075023446Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63810630883106308Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63819641260606431Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64167904686679046Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:29
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000011718
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.


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 36 20 19 20 3 3 74 35 41 11 3
Low 21 21 21 5 8 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078953   ⟹   ENSRNOP00000075077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl650,954,631 - 51,230,701 (+)Ensembl
RefSeq Acc Id: XM_006225740   ⟹   XP_006225802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera647,444,615 - 47,730,860 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594435   ⟹   XP_017449924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0651,063,794 - 51,230,860 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594436   ⟹   XP_017449925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0650,953,868 - 51,230,860 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078121   ⟹   XP_038934049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2648,242,470 - 48,545,185 (+)NCBI
RefSeq Acc Id: XM_039078122   ⟹   XP_038934050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2648,242,470 - 48,530,554 (+)NCBI
RefSeq Acc Id: XM_039078123   ⟹   XP_038934051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2648,438,731 - 48,533,322 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038934049 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934050 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934051 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006225802   ⟸   XM_006225740
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017449925   ⟸   XM_017594436
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017449924   ⟸   XM_017594435
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075077   ⟸   ENSRNOT00000078953
RefSeq Acc Id: XP_038934049   ⟸   XM_039078121
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934050   ⟸   XM_039078122
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934051   ⟸   XM_039078123
- Peptide Label: isoform X3

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 51128570 51128571 C T snv ACI/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), LE/Stm (RGD), LEW/Crl (RGD), SS/JrHsdMcwi (RGD), LL/MavRrrc (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), LEW/NCrlBR (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563296 AgrOrtholog
Ensembl Genes ENSRNOG00000056610 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000075077 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078953 UniProtKB/TrEMBL
InterPro Cog5 UniProtKB/TrEMBL
NCBI Gene 314030 ENTREZGENE
PANTHER PTHR13228 UniProtKB/TrEMBL
Pfam COG5 UniProtKB/TrEMBL
PhenoGen Cog5 PhenoGen
UniProt A0A0G2K9P5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-12 Cog5  component of oligomeric golgi complex 5  RGD1563296  similar to component of oligomeric golgi complex 5 isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563296  similar to component of oligomeric golgi complex 5 isoform 1   RGD1563296_predicted  similar to component of oligomeric golgi complex 5 isoform 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563296_predicted  similar to component of oligomeric golgi complex 5 isoform 1 (predicted)  LOC314030  similar to component of oligomeric golgi complex 5 isoform 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC314030  similar to component of oligomeric golgi complex 5 isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL