Popdc1 (popeye domain cAMP effector 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Popdc1 (popeye domain cAMP effector 1) Rattus norvegicus
Analyze
Symbol: Popdc1 (Ensembl: Bves)
Name: popeye domain cAMP effector 1 (Ensembl:blood vessel epicardial substance)
RGD ID: 1561100
Description: Predicted to enable cAMP binding activity and structural molecule activity. Predicted to be involved in several processes, including positive regulation of receptor recycling; response to ischemia; and substrate adhesion-dependent cell spreading. Predicted to act upstream of or within hematopoietic progenitor cell differentiation; regulation of heart rate; and sinoatrial node cell development. Predicted to be located in several cellular components, including bicellular tight junction; caveola; and lateral plasma membrane. Predicted to be active in sarcolemma. Human ortholog(s) of this gene implicated in autosomal recessive limb-girdle muscular dystrophy type 2X. Orthologous to human POPDC1 (popeye domain cAMP effector 1); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: blood vessel epicardial substance; Bves; popeye domain-containing 1; popeye domain-containing protein 1; popeye protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82050,401,611 - 50,442,653 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2050,401,733 - 50,442,645 (+)EnsemblGRCr8
mRatBN7.22048,819,241 - 48,860,282 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2048,822,308 - 48,857,472 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2050,565,097 - 50,600,096 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02050,214,848 - 50,249,847 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02050,899,187 - 50,934,183 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02050,439,885 - 50,474,678 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2050,439,883 - 50,474,678 (+)Ensemblrn6Rnor6.0
Rnor_5.02052,052,628 - 52,086,539 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42049,671,174 - 49,671,683 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2051,164,981 - 51,200,377 (-)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
bicellular tight junction  (IEA,ISO,ISS)
caveola  (IEA,ISO,ISS)
cell junction  (ISO)
cell projection membrane  (ISO)
lateral plasma membrane  (IEA,ISO,ISS)
membrane  (IEA,ISO,ISS)
plasma membrane  (ISO,ISS)
sarcolemma  (IBA,IEA,ISO,ISS)

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10882522   PMID:12815060   PMID:16188940   PMID:17662479   PMID:18541910   PMID:20057356   PMID:22354168   PMID:24029230   PMID:24048452   PMID:24066022   PMID:26642364   PMID:27886395  
PMID:33261556  


Genomics

Comparative Map Data
Popdc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82050,401,611 - 50,442,653 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2050,401,733 - 50,442,645 (+)EnsemblGRCr8
mRatBN7.22048,819,241 - 48,860,282 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2048,822,308 - 48,857,472 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2050,565,097 - 50,600,096 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02050,214,848 - 50,249,847 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02050,899,187 - 50,934,183 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02050,439,885 - 50,474,678 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2050,439,883 - 50,474,678 (+)Ensemblrn6Rnor6.0
Rnor_5.02052,052,628 - 52,086,539 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42049,671,174 - 49,671,683 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2051,164,981 - 51,200,377 (-)NCBICelera
Cytogenetic Map20q13NCBI
POPDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386105,096,822 - 105,137,157 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6105,096,822 - 105,137,216 (-)Ensemblhg38GRCh38
GRCh376105,544,697 - 105,585,032 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366105,651,390 - 105,691,236 (-)NCBIBuild 36Build 36hg18NCBI36
Build 346105,651,393 - 105,690,914NCBI
Celera6106,167,189 - 106,206,693 (-)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6102,987,978 - 103,028,002 (-)NCBIHuRef
CHM1_16105,806,724 - 105,846,753 (-)NCBICHM1_1
T2T-CHM13v2.06106,272,906 - 106,312,920 (-)NCBIT2T-CHM13v2.0
Popdc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391045,211,783 - 45,248,580 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1045,211,868 - 45,248,575 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381045,335,735 - 45,372,484 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1045,335,772 - 45,372,479 (+)Ensemblmm10GRCm38
MGSCv371045,055,568 - 45,089,514 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361045,024,177 - 45,058,123 (+)NCBIMGSCv36mm8
Celera1046,209,822 - 46,242,144 (+)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1023.47NCBI
Popdc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541130,517,875 - 30,551,335 (-)Ensembl
ChiLan1.0NW_00495541130,517,917 - 30,548,424 (-)NCBIChiLan1.0ChiLan1.0
POPDC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25125,111,875 - 125,156,846 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16122,998,350 - 123,043,287 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06102,915,148 - 102,951,141 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16106,784,465 - 106,822,050 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6106,787,615 - 106,822,050 (-)EnsemblpanPan2panpan1.1
BVES
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11262,542,274 - 62,581,110 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1262,545,666 - 62,579,548 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1262,331,453 - 62,369,673 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01263,393,637 - 63,432,405 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1263,393,639 - 63,432,655 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11262,748,894 - 62,787,110 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01262,590,058 - 62,628,349 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01262,868,831 - 62,907,346 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Popdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494697,512,420 - 97,548,660 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365641,788,317 - 1,823,084 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365641,791,733 - 1,823,421 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BVES
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl171,314,274 - 71,360,175 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1171,316,354 - 71,360,255 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2180,636,881 - 80,681,079 (-)NCBISscrofa10.2Sscrofa10.2susScr3
POPDC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11368,668,248 - 68,704,661 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1368,668,321 - 68,707,885 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604041,016,271 - 41,055,600 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Popdc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624952323,475 - 360,805 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624952326,812 - 360,790 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Popdc1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v13219,221,836 - 219,256,636 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Popdc1
252 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:29
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000066167
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.


QTLs in Region (GRCr8)
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)202668936256021148Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202679235356021148Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202074558556021148Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202668936256021148Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202668936256021148Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202668936256021148Rat

Markers in Region
RH143305  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map11322.3UniSTS
Cytogenetic Map20q13UniSTS
RH143833  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22048,857,447 - 48,857,705 (+)MAPPERmRatBN7.2
Rnor_6.02050,474,654 - 50,474,911NCBIRnor6.0
Rnor_5.02052,086,515 - 52,086,772UniSTSRnor5.0
RGSC_v3.42049,671,659 - 49,671,916UniSTSRGSC3.4
Celera2051,164,748 - 51,165,005UniSTS
RH 3.4 Map20511.0UniSTS
Cytogenetic Map20q13UniSTS
BI294843  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr82050,434,295 - 50,434,447 (+)Marker Load Pipeline
mRatBN7.22048,851,924 - 48,852,076 (+)MAPPERmRatBN7.2
Rnor_6.02050,468,999 - 50,469,150NCBIRnor6.0
Rnor_5.02052,081,772 - 52,081,923UniSTSRnor5.0
Celera2051,170,174 - 51,170,325UniSTS
RH 3.4 Map20502.9UniSTS
Cytogenetic Map20q13UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
15 12 67 132 68 71 40 45 40 6 283 141 11 115 79 92 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000066167
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2050,401,733 - 50,433,808 (+)Ensembl
mRatBN7.2 Ensembl2048,822,308 - 48,857,472 (+)Ensembl
Rnor_6.0 Ensembl2050,439,883 - 50,474,678 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076504
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2050,447,139 - 50,474,678 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000162385   ⟹   ENSRNOP00000105633
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2050,401,733 - 50,442,645 (+)Ensembl
RefSeq Acc Id: NM_001077590   ⟹   NP_001071058
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,404,684 - 50,439,843 (+)NCBI
mRatBN7.22048,822,312 - 48,857,472 (+)NCBI
Rnor_6.02050,439,885 - 50,474,678 (+)NCBI
Rnor_5.02052,052,628 - 52,086,539 (+)NCBI
RGSC_v3.42049,671,174 - 49,671,683 (+)RGD
Celera2051,164,981 - 51,200,377 (-)RGD
Sequence:
RefSeq Acc Id: XM_039098917   ⟹   XP_038954845
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,401,619 - 50,442,653 (+)NCBI
mRatBN7.22048,819,250 - 48,860,282 (+)NCBI
RefSeq Acc Id: XM_039098918   ⟹   XP_038954846
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,401,618 - 50,442,653 (+)NCBI
mRatBN7.22048,819,250 - 48,860,282 (+)NCBI
RefSeq Acc Id: XM_039098919   ⟹   XP_038954847
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,401,618 - 50,442,653 (+)NCBI
mRatBN7.22048,819,527 - 48,860,282 (+)NCBI
RefSeq Acc Id: XM_039098920   ⟹   XP_038954848
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,401,611 - 50,421,198 (+)NCBI
mRatBN7.22048,819,241 - 48,838,828 (+)NCBI
RefSeq Acc Id: NP_001071058   ⟸   NM_001077590
- UniProtKB: Q3BCU4 (UniProtKB/Swiss-Prot),   A6K6V1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038954848   ⟸   XM_039098920
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954846   ⟸   XM_039098918
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954845   ⟸   XM_039098917
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954847   ⟸   XM_039098919
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000105633   ⟸   ENSRNOT00000162385
Protein Domains
POPDC1-3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3BCU4-F1-model_v2 AlphaFold Q3BCU4 1-356 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561100 AgrOrtholog
BioCyc Gene G2FUF-3263 BioCyc
Ensembl Genes ENSRNOG00000043199 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000066167 ENTREZGENE
  ENSRNOT00000066167.5 UniProtKB/Swiss-Prot
  ENSRNOT00000162385 ENTREZGENE
Gene3D-CATH 2.60.120.10 UniProtKB/Swiss-Prot
InterPro cNMP-bd-like UniProtKB/Swiss-Prot
  POPDC1-3_dom UniProtKB/Swiss-Prot
  Popeye_prot UniProtKB/Swiss-Prot
  RmlC-like_jellyroll UniProtKB/Swiss-Prot
KEGG Report rno:365603 UniProtKB/Swiss-Prot
NCBI Gene 365603 ENTREZGENE
PANTHER BLOOD VESSEL EPICARDIAL SUBSTANCE UniProtKB/Swiss-Prot
  PTHR12101 UniProtKB/Swiss-Prot
Pfam Popeye UniProtKB/Swiss-Prot
PhenoGen Popdc1 PhenoGen
RatGTEx ENSRNOG00000043199 RatGTEx
Superfamily-SCOP SSF51206 UniProtKB/Swiss-Prot
UniProt A6K6V1 ENTREZGENE, UniProtKB/TrEMBL
  POPD1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-11-08 Popdc1  popeye domain cAMP effector 1  Bves  blood vessel epicardial substance  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 Bves  blood vessel epicardial substance      Symbol and Name status set to provisional 70820 PROVISIONAL