Golga4 (golgin A4) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Golga4 (golgin A4) Rattus norvegicus
Analyze
Symbol: Golga4
Name: golgin A4
RGD ID: 1591925
Description: Predicted to have GTPase binding activity. Predicted to be involved in Golgi to plasma membrane protein transport and positive regulation of axon extension. Predicted to localize to Golgi apparatus and nucleoplasm. Orthologous to human GOLGA4 (golgin A4); INTERACTS WITH 17alpha-ethynylestradiol; bisphenol A; cisplatin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: golgi autoantigen, golgin subfamily a, 4; Golgin subfamily A member 4; LOC501069; similar to golgi autoantigen golgin subtype a4; tGolgin-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
mRatBN7.28118,208,200 - 118,285,003 (+)NCBI
Rnor_6.0 Ensembl8127,171,537 - 127,248,538 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08127,171,221 - 127,248,938 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08126,393,530 - 126,471,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48123,404,540 - 123,504,104 (+)NCBIRGSC3.4rn4RGSC3.4
Celera8117,393,586 - 117,470,254 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
Golgi apparatus  (IBA,IEA,ISO)
Golgi membrane  (IEA)
membrane  (IEA)
nucleoplasm  (IEA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:12162805   PMID:12477932   PMID:14580338   PMID:15265687   PMID:18570454   PMID:19224922   PMID:22705394  


Genomics

Comparative Map Data
Golga4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28118,208,200 - 118,285,003 (+)NCBI
Rnor_6.0 Ensembl8127,171,537 - 127,248,538 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08127,171,221 - 127,248,938 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08126,393,530 - 126,471,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48123,404,540 - 123,504,104 (+)NCBIRGSC3.4rn4RGSC3.4
Celera8117,393,586 - 117,470,254 (+)NCBICelera
Cytogenetic Map8q32NCBI
GOLGA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl337,243,177 - 37,366,751 (+)EnsemblGRCh38hg38GRCh38
GRCh38337,243,269 - 37,366,879 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37337,284,762 - 37,408,370 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37337,284,682 - 37,408,370 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36337,259,742 - 37,383,246 (+)NCBINCBI36hg18NCBI36
Build 34337,259,741 - 37,383,245NCBI
Celera337,218,214 - 37,341,938 (+)NCBI
Cytogenetic Map3p22.2NCBI
HuRef337,225,865 - 37,349,347 (+)NCBIHuRef
CHM1_1337,236,284 - 37,359,981 (+)NCBICHM1_1
Golga4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399118,335,280 - 118,411,587 (+)NCBIGRCm39mm39
GRCm389118,506,196 - 118,582,519 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9118,506,267 - 118,582,519 (+)EnsemblGRCm38mm10GRCm38
MGSCv379118,415,436 - 118,491,637 (+)NCBIGRCm37mm9NCBIm37
MGSCv369118,355,016 - 118,431,217 (+)NCBImm8
Celera9118,976,652 - 119,052,515 (+)NCBICelera
Cytogenetic Map9F3NCBI
Golga4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554214,131,653 - 4,243,651 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554214,130,040 - 4,251,968 (+)NCBIChiLan1.0ChiLan1.0
GOLGA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1337,437,626 - 37,556,908 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl337,442,669 - 37,545,634 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0337,149,793 - 37,269,709 (+)NCBIMhudiblu_PPA_v0panPan3
GOLGA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl237,106,342 - 7,232,624 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1237,106,051 - 7,232,628 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Golga4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647326,741,548 - 26,838,342 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GOLGA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1322,125,121 - 22,250,466 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11322,125,131 - 22,250,465 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21324,019,468 - 24,143,177 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GOLGA4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1152,046,436 - 2,162,590 (-)NCBI
ChlSab1.1 Ensembl152,046,156 - 2,162,235 (-)Ensembl
Golga4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624890931,878 - 938,932 (+)NCBI

Position Markers
D8Rat2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08127,182,508 - 127,182,642NCBIRnor6.0
Rnor_5.08126,404,814 - 126,404,948UniSTSRnor5.0
RGSC_v3.48123,415,271 - 123,415,406RGDRGSC3.4
RGSC_v3.48123,415,272 - 123,415,406UniSTSRGSC3.4
RGSC_v3.18123,435,009 - 123,435,143RGD
Celera8117,404,316 - 117,404,450UniSTS
RH 3.4 Map81303.7UniSTS
RH 3.4 Map81303.7RGD
RH 2.0 Map81024.7RGD
SHRSP x BN Map881.9299RGD
FHH x ACI Map886.7699RGD
Cytogenetic Map8q32UniSTS
RH143454  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08127,186,031 - 127,186,161NCBIRnor6.0
Rnor_5.08126,408,337 - 126,408,467UniSTSRnor5.0
RGSC_v3.48123,418,795 - 123,418,925UniSTSRGSC3.4
Celera8117,407,839 - 117,407,969UniSTS
RH 3.4 Map81302.6UniSTS
Cytogenetic Map8q32UniSTS
RH129880  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08127,248,567 - 127,248,778NCBIRnor6.0
Rnor_5.08126,470,873 - 126,471,084UniSTSRnor5.0
RGSC_v3.48123,504,133 - 123,504,344UniSTSRGSC3.4
Celera8117,470,283 - 117,470,494UniSTS
RH 3.4 Map81292.1UniSTS
Cytogenetic Map8q32UniSTS
RH138253  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08127,224,198 - 127,224,335NCBIRnor6.0
Rnor_5.08126,446,504 - 126,446,641UniSTSRnor5.0
RGSC_v3.48123,479,764 - 123,479,901UniSTSRGSC3.4
Celera8117,445,926 - 117,446,063UniSTS
RH 3.4 Map81291.9UniSTS
Cytogenetic Map8q32UniSTS
RH139299  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08127,211,949 - 127,212,108NCBIRnor6.0
Rnor_5.08126,434,255 - 126,434,414UniSTSRnor5.0
RGSC_v3.48123,467,302 - 123,467,461UniSTSRGSC3.4
Celera8117,433,814 - 117,433,973UniSTS
RH 3.4 Map81290.4UniSTS
Cytogenetic Map8q32UniSTS
RH135993  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08127,248,636 - 127,248,804NCBIRnor6.0
Rnor_5.08126,470,942 - 126,471,110UniSTSRnor5.0
RGSC_v3.48123,504,202 - 123,504,370UniSTSRGSC3.4
Celera8117,470,352 - 117,470,520UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)876103982127182642Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat
1599689Iddm24Insulin dependent diabetes mellitus QTL 244.720.001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)8120870965127609447Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:51
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000051290
Prediction methods: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.


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000051290   ⟹   ENSRNOP00000039533
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8127,171,636 - 127,248,310 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078625   ⟹   ENSRNOP00000069066
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8127,171,537 - 127,248,511 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087753   ⟹   ENSRNOP00000075007
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8127,171,636 - 127,248,538 (+)Ensembl
RefSeq Acc Id: NM_001191080   ⟹   NP_001178009
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28118,208,200 - 118,285,003 (+)NCBI
Rnor_6.08127,171,636 - 127,248,538 (+)NCBI
Rnor_5.08126,393,530 - 126,471,244 (+)NCBI
Celera8117,393,586 - 117,470,254 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244126   ⟹   XP_006244188
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,395 - 127,248,935 (+)NCBI
Rnor_5.08126,393,530 - 126,471,244 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244132   ⟹   XP_006244194
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,395 - 127,248,538 (+)NCBI
Rnor_5.08126,393,530 - 126,471,244 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244133   ⟹   XP_006244195
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,395 - 127,248,935 (+)NCBI
Rnor_5.08126,393,530 - 126,471,244 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595852   ⟹   XP_017451341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,394 - 127,248,935 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595853   ⟹   XP_017451342
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,394 - 127,248,938 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595854   ⟹   XP_017451343
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,615 - 127,248,938 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595855   ⟹   XP_017451344
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,394 - 127,243,078 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595856   ⟹   XP_017451345
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,394 - 127,248,938 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595857   ⟹   XP_017451346
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,395 - 127,248,938 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595858   ⟹   XP_017451347
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,171,221 - 127,248,938 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178009 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85124 (Get FASTA)   NCBI Sequence Viewer  
  Q5U4E6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178009   ⟸   NM_001191080
- UniProtKB: A0A0G2K9I3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244194   ⟸   XM_006244132
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006244188   ⟸   XM_006244126
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006244195   ⟸   XM_006244133
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017451347   ⟸   XM_017595858
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017451342   ⟸   XM_017595853
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017451345   ⟸   XM_017595856
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017451341   ⟸   XM_017595852
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451344   ⟸   XM_017595855
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017451346   ⟸   XM_017595857
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017451343   ⟸   XM_017595854
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000075007   ⟸   ENSRNOT00000087753
RefSeq Acc Id: ENSRNOP00000039533   ⟸   ENSRNOT00000051290
RefSeq Acc Id: ENSRNOP00000069066   ⟸   ENSRNOT00000078625
Protein Domains
GRIP

Transcriptome

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

Promoters
RGD ID:13696364
Promoter ID:EPDNEW_R6887
Type:multiple initiation site
Name:Golga4_1
Description:golgin A4
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_6.08127,171,672 - 127,171,732EPDNEW

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_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 126413019 126413020 A G snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), MNS/Gib (KNAW), WN/N (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU)
8 126448632 126448633 C T snv SHR/OlaIpcv (KNAW), SHR/NHsd (KNAW), SHR/NCrlPrin (KNAW), SHRSP/Gcrc (KNAW), SHR/OlaIpcvPrin (KNAW)
8 126449307 126449308 G A snv LN/MavRrrc (KNAW), MHS/Gib (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), F344/NRrrc (Illumina) (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), BUF/MNa (KyushuU), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), F344/Jcl (KyushuU), LL/MavRrrc (KNAW), LH/MavRrrc (KNAW), SS/JrHsdMcwi (MCW), ZF (KyushuU), GH/OmrMcwi (MCW), SR/JrHsd (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 127190713 127190714 A G snv ACI/EurMcwi (MCW), WKY/NHsd (RGD), COP/CrCrl (MCW & UW), WKY/Gcrc (RGD), WKY/NCrl (RGD), WAG/Rij (RGD), SS/JrHsdMcwi (RGD), SS/Jr (RGD), SR/JrHsd (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), SBN/Ygl (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), MHS/Gib (RGD), LL/MavRrrc (RGD), LN/MavRrrc (RGD), LH/MavRrrc (RGD), LEW/NCrlBR (RGD), LEW/Crl (RGD), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, CDS, ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), WKY/N (MCW), FHL/EurMcwi (RGD), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), GK/Ox (RGD), LE/Stm (RGD)
8 127226326 127226327 C T snv SHR/NHsd (RGD), SHRSP/Gcrc (RGD)
8 127227001 127227002 G A snv MNS/Gib (RGD), LEW/Crl (RGD), SR/JrHsd (RGD), CDR, MHS/Gib (RGD), GH/OmrMcwi (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), F344/NCrl (RGD), LN/MavRrrc (RGD), SS/JrHsdMcwi (RGD), LH/MavRrrc (RGD), SS/Jr (RGD), F344/NRrrc (MCW), LEW/NCrlBR (RGD), LL/MavRrrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1591925 AgrOrtholog
Ensembl Genes ENSRNOG00000029910 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039533 UniProtKB/Swiss-Prot
  ENSRNOP00000069066 UniProtKB/TrEMBL
  ENSRNOP00000075007 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051290 UniProtKB/Swiss-Prot
  ENSRNOT00000078625 UniProtKB/TrEMBL
  ENSRNOT00000087753 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123209 IMAGE-MGC_LOAD
InterPro GRIP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:501069 UniProtKB/TrEMBL
MGC_CLONE MGC:105866 IMAGE-MGC_LOAD
NCBI Gene 501069 ENTREZGENE
Pfam GRIP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Golga4 PhenoGen
PROSITE GRIP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Grip UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JUE4_RAT UniProtKB/TrEMBL
  A0A0G2K9I3 ENTREZGENE, UniProtKB/TrEMBL
  GOGA4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Golga4  golgin A4  Golga4  golgi autoantigen, golgin subfamily a, 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Golga4  golgi autoantigen, golgin subfamily a, 4  LOC501069  similar to golgi autoantigen golgin subtype a4; tGolgin-1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC501069  similar to golgi autoantigen golgin subtype a4; tGolgin-1      Symbol and Name status set to provisional 70820 PROVISIONAL