Popdc3 (popeye domain containing 3) - Rat Genome Database

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Gene: Popdc3 (popeye domain containing 3) Rattus norvegicus
Analyze
Symbol: Popdc3
Name: popeye domain containing 3
RGD ID: 1590760
Description: Predicted to enable cAMP binding activity. Predicted to be involved in several processes, including heart development; skeletal muscle tissue development; and striated muscle cell differentiation. Predicted to be located in membrane. Predicted to be active in sarcolemma. Human ortholog(s) of this gene implicated in autosomal recessive limb-girdle muscular dystrophy. Orthologous to human POPDC3 (popeye domain containing 3); INTERACTS WITH bisphenol A; Cuprizon; 17beta-estradiol (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC641520; popeye domain-containing 3; popeye domain-containing protein 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82050,354,775 - 50,383,050 (+)NCBIGRCr8
mRatBN7.22048,772,397 - 48,800,677 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2048,772,462 - 48,800,593 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2050,515,094 - 50,543,186 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02050,164,847 - 50,192,937 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02050,849,177 - 50,877,267 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02050,394,617 - 50,422,551 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2050,394,650 - 50,422,560 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02052,006,146 - 52,033,991 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2051,221,107 - 51,249,040 (-)NCBICelera
Cytogenetic Map20q13NCBI
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
membrane  (ISO)
sarcolemma  (IBA)

Molecular Function
cAMP binding  (IBA,ISO)

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:12477932   PMID:17662479   PMID:22354168  


Genomics

Comparative Map Data
Popdc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82050,354,775 - 50,383,050 (+)NCBIGRCr8
mRatBN7.22048,772,397 - 48,800,677 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2048,772,462 - 48,800,593 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2050,515,094 - 50,543,186 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02050,164,847 - 50,192,937 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02050,849,177 - 50,877,267 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02050,394,617 - 50,422,551 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2050,394,650 - 50,422,560 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02052,006,146 - 52,033,991 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2051,221,107 - 51,249,040 (-)NCBICelera
Cytogenetic Map20q13NCBI
POPDC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386105,157,900 - 105,180,014 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6105,157,900 - 105,180,014 (-)EnsemblGRCh38hg38GRCh38
GRCh376105,605,775 - 105,627,889 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366105,712,470 - 105,734,563 (-)NCBINCBI36Build 36hg18NCBI36
Build 346105,712,469 - 105,734,563NCBI
Celera6106,227,913 - 106,249,989 (-)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6103,048,673 - 103,070,745 (-)NCBIHuRef
CHM1_16105,867,475 - 105,889,561 (-)NCBICHM1_1
T2T-CHM13v2.06106,333,653 - 106,355,749 (-)NCBIT2T-CHM13v2.0
Popdc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391045,165,401 - 45,194,546 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1045,054,194 - 45,194,548 (+)EnsemblGRCm39 Ensembl
GRCm381045,289,305 - 45,318,450 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1045,178,098 - 45,318,452 (+)EnsemblGRCm38mm10GRCm38
MGSCv371045,009,111 - 45,038,256 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361044,977,720 - 45,006,865 (+)NCBIMGSCv36mm8
Celera1046,163,076 - 46,192,460 (+)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1023.35NCBI
Popdc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541130,564,194 - 30,571,767 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541130,566,988 - 30,573,158 (-)NCBIChiLan1.0ChiLan1.0
POPDC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25125,177,888 - 125,199,634 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16123,064,377 - 123,086,092 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06102,972,263 - 102,993,986 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16106,846,321 - 106,864,675 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6106,846,329 - 106,850,599 (-)Ensemblpanpan1.1panPan2
POPDC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11262,597,020 - 62,615,062 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1262,484,472 - 62,601,339 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1262,385,191 - 62,403,247 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01263,447,955 - 63,466,023 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1263,447,955 - 63,466,028 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11262,802,847 - 62,820,916 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01262,644,090 - 62,662,157 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01262,923,296 - 62,941,390 (-)NCBIUU_Cfam_GSD_1.0
Popdc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494697,565,101 - 97,586,052 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365641,840,458 - 1,843,492 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365641,840,270 - 1,860,894 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POPDC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl171,380,770 - 71,400,191 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1171,380,760 - 71,400,134 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2180,701,627 - 80,720,992 (-)NCBISscrofa10.2Sscrofa10.2susScr3
POPDC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11368,630,236 - 68,652,699 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1368,648,685 - 68,652,710 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604040,977,802 - 41,000,331 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Popdc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624952381,134 - 385,794 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624952381,543 - 403,907 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Popdc3
308 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:102
Count of miRNA genes:77
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000073259
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat

Markers in Region
D20Got42  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22048,787,890 - 48,788,164 (+)MAPPERmRatBN7.2
Rnor_6.02050,410,082 - 50,410,355NCBIRnor6.0
Rnor_5.02052,021,522 - 52,021,795UniSTSRnor5.0
Celera2051,233,284 - 51,233,557UniSTS
RH 3.4 Map20502.9RGD
RH 3.4 Map20502.9UniSTS
RH 2.0 Map20614.8RGD
RH133788  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map20501.6UniSTS


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 24 8 11 8
Low 1 19 4 4 4 74 18 33 11
Below cutoff 2 25 14 10 14 15 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000073259   ⟹   ENSRNOP00000066864
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2048,772,462 - 48,800,360 (+)Ensembl
Rnor_6.0 Ensembl2050,394,673 - 50,422,551 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076010   ⟹   ENSRNOP00000068483
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2050,394,650 - 50,422,541 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077065   ⟹   ENSRNOP00000068135
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2048,796,923 - 48,800,593 (+)Ensembl
Rnor_6.0 Ensembl2050,394,654 - 50,422,560 (+)Ensembl
RefSeq Acc Id: NM_001037369   ⟹   NP_001032446
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,354,775 - 50,383,050 (+)NCBI
mRatBN7.22048,772,397 - 48,800,677 (+)NCBI
Rnor_6.02050,394,673 - 50,422,551 (+)NCBI
Rnor_5.02052,006,146 - 52,033,991 (+)NCBI
Celera2051,221,107 - 51,249,040 (-)RGD
Sequence:
RefSeq Acc Id: NM_001415671   ⟹   NP_001402600
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82050,354,775 - 50,383,050 (+)NCBI
mRatBN7.22048,772,397 - 48,800,677 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001032446   ⟸   NM_001037369
- Peptide Label: isoform 2
- UniProtKB: Q3KRE1 (UniProtKB/TrEMBL),   Q3BCU3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068135   ⟸   ENSRNOT00000077065
RefSeq Acc Id: ENSRNOP00000066864   ⟸   ENSRNOT00000073259
RefSeq Acc Id: ENSRNOP00000068483   ⟸   ENSRNOT00000076010
RefSeq Acc Id: NP_001402600   ⟸   NM_001415671
- Peptide Label: isoform 1
- UniProtKB: A0A096MJH9 (UniProtKB/TrEMBL),   A6K6V3 (UniProtKB/TrEMBL),   Q3BCU3 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MJH9-F1-model_v2 AlphaFold A0A096MJH9 1-291 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:1590760 AgrOrtholog
BioCyc Gene G2FUF-3264 BioCyc
Ensembl Genes ENSRNOG00000047102 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073259 ENTREZGENE
  ENSRNOT00000073259.3 UniProtKB/TrEMBL
  ENSRNOT00000077065 ENTREZGENE
  ENSRNOT00000077065.3 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5623862 IMAGE-MGC_LOAD
InterPro cNMP-bd-like UniProtKB/TrEMBL
  Popeye_prot UniProtKB/TrEMBL
KEGG Report rno:641520 UniProtKB/TrEMBL
MGC_CLONE MGC:124663 IMAGE-MGC_LOAD
NCBI Gene 641520 ENTREZGENE
PANTHER Popeye UniProtKB/TrEMBL
  POPEYE DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
Pfam Popeye UniProtKB/TrEMBL
PhenoGen Popdc3 PhenoGen
RatGTEx ENSRNOG00000047102 RatGTEx
Superfamily-SCOP SSF51206 UniProtKB/TrEMBL
UniProt A0A096MJH9 ENTREZGENE, UniProtKB/TrEMBL
  A6K6V3 ENTREZGENE, UniProtKB/TrEMBL
  Q3BCU3 ENTREZGENE, UniProtKB/TrEMBL
  Q3KRE1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-09 Popdc3  popeye domain containing 3  LOC641520  popeye domain-containing 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC641520  popeye domain-containing 3      Symbol and Name status set to provisional 70820 PROVISIONAL