Gopc (golgi associated PDZ and coiled-coil motif containing) - Rat Genome Database

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Gene: Gopc (golgi associated PDZ and coiled-coil motif containing) Rattus norvegicus
Analyze
Symbol: Gopc
Name: golgi associated PDZ and coiled-coil motif containing
RGD ID: 1309512
Description: Predicted to enable several functions, including frizzled binding activity; protein homodimerization activity; and transmembrane transporter binding activity. Predicted to be involved in negative regulation of anion channel activity and negative regulation of protein localization to cell surface. Predicted to act upstream of or within spermatid nucleus differentiation. Predicted to be located in several cellular components, including Golgi apparatus; synapse; and trans-Golgi network transport vesicle. Predicted to be part of protein-containing complex. Orthologous to human GOPC (golgi associated PDZ and coiled-coil motif containing); INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC309774
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
GRCr82032,270,314 - 32,319,635 (-)NCBIGRCr8
mRatBN7.22031,727,617 - 31,776,904 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,727,620 - 31,776,903 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2032,726,053 - 32,781,732 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02032,116,963 - 32,172,643 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02032,853,588 - 32,902,883 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02033,471,355 - 33,521,281 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2033,471,351 - 33,521,311 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02035,250,254 - 35,299,353 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42031,055,284 - 31,105,701 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12031,071,736 - 31,119,338 (-)NCBI
Celera2033,125,468 - 33,174,815 (-)NCBICelera
Cytogenetic Map20q11NCBI
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

Cellular Component

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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11162552   PMID:11384996   PMID:11520064   PMID:11707463   PMID:12372286   PMID:12477932   PMID:15458844   PMID:16765935   PMID:18468998   PMID:19860857   PMID:21953547   PMID:34383253  


Genomics

Comparative Map Data
Gopc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82032,270,314 - 32,319,635 (-)NCBIGRCr8
mRatBN7.22031,727,617 - 31,776,904 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,727,620 - 31,776,903 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2032,726,053 - 32,781,732 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02032,116,963 - 32,172,643 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02032,853,588 - 32,902,883 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02033,471,355 - 33,521,281 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2033,471,351 - 33,521,311 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02035,250,254 - 35,299,353 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42031,055,284 - 31,105,701 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12031,071,736 - 31,119,338 (-)NCBI
Celera2033,125,468 - 33,174,815 (-)NCBICelera
Cytogenetic Map20q11NCBI
GOPC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386117,560,269 - 117,602,511 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6117,560,269 - 117,602,542 (-)EnsemblGRCh38hg38GRCh38
GRCh376117,881,432 - 117,923,674 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366117,988,125 - 118,030,374 (-)NCBINCBI36Build 36hg18NCBI36
Build 346117,991,109 - 118,030,220NCBI
Celera6118,624,329 - 118,666,606 (-)NCBICelera
Cytogenetic Map6q22.1NCBI
HuRef6115,462,063 - 115,504,349 (-)NCBIHuRef
CHM1_16118,145,375 - 118,187,647 (-)NCBICHM1_1
T2T-CHM13v2.06118,744,505 - 118,786,752 (-)NCBIT2T-CHM13v2.0
Gopc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391052,213,120 - 52,258,220 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1052,211,946 - 52,258,220 (-)EnsemblGRCm39 Ensembl
GRCm381052,337,024 - 52,382,124 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1052,335,850 - 52,382,124 (-)EnsemblGRCm38mm10GRCm38
MGSCv371052,056,887 - 52,101,881 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361052,025,496 - 52,070,490 (-)NCBIMGSCv36mm8
Celera1053,174,463 - 53,219,811 (-)NCBICelera
Cytogenetic Map10B3NCBI
cM Map1026.54NCBI
Gopc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955436742,305 - 777,566 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955436743,616 - 777,878 (-)NCBIChiLan1.0ChiLan1.0
GOPC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25137,574,230 - 137,619,713 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16135,467,252 - 135,512,718 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06115,368,682 - 115,411,140 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16119,509,936 - 119,552,010 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6119,509,936 - 119,552,010 (-)Ensemblpanpan1.1panPan2
GOPC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1157,790,118 - 57,829,022 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl157,792,647 - 57,828,820 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha158,589,110 - 58,629,156 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0157,970,112 - 58,010,164 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl157,970,099 - 58,011,073 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1157,871,500 - 57,911,541 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0157,712,463 - 57,752,507 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0158,343,632 - 58,383,890 (-)NCBIUU_Cfam_GSD_1.0
Gopc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946108,509,927 - 108,548,999 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936658614,476 - 655,905 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936658614,711 - 655,874 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GOPC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl144,239,383 - 44,287,198 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1144,239,364 - 44,285,886 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2149,584,131 - 49,631,566 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GOPC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11356,229,780 - 56,270,829 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1356,229,810 - 56,272,830 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604028,567,387 - 28,608,428 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gopc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479812,188,635 - 12,218,305 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479812,188,460 - 12,216,542 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gopc
350 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:350
Count of miRNA genes:199
Interacting mature miRNAs:267
Transcripts:ENSRNOT00000057476
Prediction methods:Miranda, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203161428444396023Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat

Markers in Region
BE108698  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22031,736,516 - 31,736,676 (+)MAPPERmRatBN7.2
Rnor_6.02033,480,590 - 33,480,749NCBIRnor6.0
Rnor_5.02035,259,489 - 35,259,648UniSTSRnor5.0
RGSC_v3.42031,064,177 - 31,064,336UniSTSRGSC3.4
Celera2033,134,332 - 33,134,491UniSTS
RH 3.4 Map20308.84UniSTS
Cytogenetic Map20q11UniSTS
RH134823  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22031,727,829 - 31,728,011 (+)MAPPERmRatBN7.2
Rnor_6.02033,471,561 - 33,471,742NCBIRnor6.0
Rnor_5.02035,250,460 - 35,250,641UniSTSRnor5.0
RGSC_v3.42031,055,490 - 31,055,671UniSTSRGSC3.4
Celera2033,125,674 - 33,125,855UniSTS
Cytogenetic Map20q11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000057476   ⟹   ENSRNOP00000054286
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2031,727,620 - 31,776,903 (-)Ensembl
Rnor_6.0 Ensembl2033,471,351 - 33,521,311 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000083295   ⟹   ENSRNOP00000070262
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2031,748,676 - 31,776,903 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000102347   ⟹   ENSRNOP00000079115
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2031,727,620 - 31,745,384 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000110578   ⟹   ENSRNOP00000082400
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2031,727,620 - 31,776,903 (-)Ensembl
RefSeq Acc Id: NM_001107631   ⟹   NP_001101101
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82032,270,314 - 32,319,611 (-)NCBI
mRatBN7.22031,727,617 - 31,776,904 (-)NCBI
Rnor_6.02033,471,355 - 33,521,281 (-)NCBI
Rnor_5.02035,250,254 - 35,299,353 (-)NCBI
RGSC_v3.42031,055,284 - 31,105,701 (-)RGD
Celera2033,125,468 - 33,174,815 (-)RGD
Sequence:
RefSeq Acc Id: NM_001393720   ⟹   NP_001380649
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82032,270,314 - 32,319,611 (-)NCBI
mRatBN7.22031,727,617 - 31,776,904 (-)NCBI
RefSeq Acc Id: XR_010060701
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82032,275,583 - 32,319,635 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001101101 (Get FASTA)   NCBI Sequence Viewer  
  NP_001380649 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68160 (Get FASTA)   NCBI Sequence Viewer  
  EDL92940 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000054286.4
  ENSRNOP00000070262.2
  ENSRNOP00000079115.1
  ENSRNOP00000082400.1
RefSeq Acc Id: NP_001101101   ⟸   NM_001107631
- Peptide Label: isoform 2
- UniProtKB: A0A8J8YNI6 (UniProtKB/TrEMBL),   A0A8I5ZTW6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000054286   ⟸   ENSRNOT00000057476
Ensembl Acc Id: ENSRNOP00000079115   ⟸   ENSRNOT00000102347
Ensembl Acc Id: ENSRNOP00000070262   ⟸   ENSRNOT00000083295
Ensembl Acc Id: ENSRNOP00000082400   ⟸   ENSRNOT00000110578
RefSeq Acc Id: NP_001380649   ⟸   NM_001393720
- Peptide Label: isoform 1
- UniProtKB: A0A8I5ZTW6 (UniProtKB/TrEMBL)
Protein Domains
PDZ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B4F775-F1-model_v2 AlphaFold B4F775 1-308 view protein structure

Transcriptome

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

Promoters
RGD ID:13701624
Promoter ID:EPDNEW_R12148
Type:multiple initiation site
Name:Gopc_1
Description:golgi associated PDZ and coiled-coil motif containing
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_6.02033,521,315 - 33,521,375EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309512 AgrOrtholog
BioCyc Gene G2FUF-3646 BioCyc
Ensembl Genes ENSRNOG00000000408 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057476.4 UniProtKB/TrEMBL
  ENSRNOT00000083295.2 UniProtKB/TrEMBL
  ENSRNOT00000102347.1 UniProtKB/TrEMBL
  ENSRNOT00000110578.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/TrEMBL
InterPro GOPC UniProtKB/TrEMBL
  PDZ/DHR/GLGF UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
KEGG Report rno:309774 UniProtKB/TrEMBL
NCBI Gene 309774 ENTREZGENE
PANTHER GOLGI-ASSOCIATED PDZ AND COILED-COIL MOTIF-CONTAINING PROTEIN UniProtKB/TrEMBL
  PTHR16528 UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
PhenoGen Gopc PhenoGen
PROSITE PDZ UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000408 RatGTEx
SMART PDZ UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt A0A0G2JXG5_RAT UniProtKB/TrEMBL
  A0A8I5ZMA7_RAT UniProtKB/TrEMBL
  A0A8I5ZTW6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8J8YNI6 ENTREZGENE, UniProtKB/TrEMBL
  B4F775_RAT UniProtKB/TrEMBL
UniProt Secondary F1LSN7 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Gopc  golgi associated PDZ and coiled-coil motif containing   Gopc_predicted  golgi associated PDZ and coiled-coil motif containing (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Gopc_predicted  golgi associated PDZ and coiled-coil motif containing (predicted)      Symbol and Name status set to approved 70820 APPROVED