Popdc2 (popeye domain containing 2) - Rat Genome Database

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Gene: Popdc2 (popeye domain containing 2) Rattus norvegicus
Analyze
Symbol: Popdc2
Name: popeye domain containing 2
RGD ID: 735226
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 act upstream of or within regulation of heart rate and sinoatrial node cell development. Predicted to be located in membrane. Predicted to be active in sarcolemma. Orthologous to human POPDC2 (popeye domain containing 2); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC100910206; MGC72601; popeye domain-containing protein 2; popeye domain-containing protein 2-like
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
mRatBN7.21162,351,843 - 62,398,688 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1162,374,759 - 62,390,756 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1171,187,283 - 71,203,279 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01163,849,530 - 63,865,526 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01162,899,864 - 62,915,862 (-)NCBIRnor_WKY
Rnor_6.01164,915,041 - 64,954,704 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1164,936,692 - 64,952,687 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01167,129,306 - 67,151,642 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41164,154,286 - 64,170,282 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11164,211,875 - 64,227,871 (-)NCBI
Celera1161,876,220 - 61,892,242 (-)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (ISO)
sarcolemma  (IBA,ISO)

Molecular Function
cAMP binding  (IBA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Isolation and characterization of the novel popeye gene family expressed in skeletal muscle and heart. Andree B, etal., Dev Biol 2000 Jul 15;223(2):371-82.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:17662479   PMID:22354168   PMID:26642364   PMID:28755400   PMID:31505169   PMID:33261556  


Genomics

Comparative Map Data
Popdc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21162,351,843 - 62,398,688 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1162,374,759 - 62,390,756 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1171,187,283 - 71,203,279 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01163,849,530 - 63,865,526 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01162,899,864 - 62,915,862 (-)NCBIRnor_WKY
Rnor_6.01164,915,041 - 64,954,704 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1164,936,692 - 64,952,687 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01167,129,306 - 67,151,642 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41164,154,286 - 64,170,282 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11164,211,875 - 64,227,871 (-)NCBI
Celera1161,876,220 - 61,892,242 (-)NCBICelera
Cytogenetic Map11q21NCBI
POPDC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383119,642,056 - 119,660,883 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl3119,636,457 - 119,665,324 (-)EnsemblGRCh38hg38GRCh38
GRCh373119,360,903 - 119,379,436 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363120,843,596 - 120,862,094 (-)NCBINCBI36Build 36hg18NCBI36
Build 343120,843,597 - 120,862,094NCBI
Celera3117,769,457 - 117,787,954 (-)NCBICelera
Cytogenetic Map3q13.33NCBI
HuRef3116,736,572 - 116,755,066 (-)NCBIHuRef
CHM1_13119,324,408 - 119,342,901 (-)NCBICHM1_1
T2T-CHM13v2.03122,361,759 - 122,380,289 (-)NCBIT2T-CHM13v2.0
Popdc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391638,182,523 - 38,198,578 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1638,182,571 - 38,198,578 (+)EnsemblGRCm39 Ensembl
GRCm381638,362,161 - 38,378,216 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1638,362,209 - 38,378,216 (+)EnsemblGRCm38mm10GRCm38
MGSCv371638,362,259 - 38,378,302 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361638,281,484 - 38,297,455 (+)NCBIMGSCv36mm8
Celera1638,772,441 - 38,788,493 (+)NCBICelera
Cytogenetic Map16B3NCBI
Popdc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542719,345,226 - 19,367,759 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542719,347,880 - 19,367,759 (-)NCBIChiLan1.0ChiLan1.0
POPDC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13123,673,815 - 123,692,684 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3123,673,815 - 123,692,684 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03116,761,474 - 116,780,369 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
POPDC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13323,275,666 - 23,295,413 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3323,276,455 - 23,295,088 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3323,306,245 - 23,325,293 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03323,513,597 - 23,533,028 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3323,514,929 - 23,548,542 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13323,316,273 - 23,335,538 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03323,352,389 - 23,370,898 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03323,921,853 - 23,941,107 (-)NCBIUU_Cfam_GSD_1.0
Popdc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602130,939,491 - 130,958,507 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365366,560,329 - 6,582,331 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365366,562,583 - 6,582,407 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POPDC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13140,601,515 - 140,620,789 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113140,601,522 - 140,621,928 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213149,932,130 - 149,951,356 (+)NCBISscrofa10.2Sscrofa10.2susScr3
POPDC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12261,160,174 - 61,178,838 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2261,160,413 - 61,178,414 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041105,133,456 - 105,151,992 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Popdc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473128,493,230 - 28,523,157 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473128,490,489 - 28,521,611 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Popdc2
201 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:328
Count of miRNA genes:188
Interacting mature miRNAs:223
Transcripts:ENSRNOT00000003999
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat

Markers in Region
RH129757  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21162,374,785 - 62,374,966 (+)MAPPERmRatBN7.2
Rnor_6.01164,936,719 - 64,936,899NCBIRnor6.0
Rnor_5.01167,149,589 - 67,149,769UniSTSRnor5.0
RGSC_v3.41164,154,314 - 64,154,494UniSTSRGSC3.4
Celera1161,876,248 - 61,876,428UniSTS
RH 3.4 Map11508.7UniSTS
Cytogenetic Map11q21UniSTS


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 8 11 4 11 8
Low 42 26 19 26 74 33 37
Below cutoff 15 15 15 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000087892   ⟹   ENSRNOP00000071721
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1162,374,759 - 62,390,756 (-)Ensembl
Rnor_6.0 Ensembl1164,936,692 - 64,952,687 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095198   ⟹   ENSRNOP00000087674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1162,375,545 - 62,390,756 (-)Ensembl
RefSeq Acc Id: NM_199113   ⟹   NP_954544
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,374,758 - 62,390,756 (-)NCBI
Rnor_6.01164,936,691 - 64,952,687 (-)NCBI
Rnor_5.01167,129,306 - 67,151,642 (+)NCBI
RGSC_v3.41164,154,286 - 64,170,282 (-)RGD
Celera1161,876,220 - 61,892,242 (-)RGD
Sequence:
RefSeq Acc Id: XM_008768733   ⟹   XP_008766955
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,371,985 - 62,391,589 (-)NCBI
Rnor_6.01164,936,696 - 64,954,704 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008768734   ⟹   XP_008766956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,351,843 - 62,391,590 (-)NCBI
Rnor_6.01164,915,041 - 64,954,704 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598027   ⟹   XP_017453516
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,371,985 - 62,391,575 (-)NCBI
Rnor_6.01164,936,696 - 64,954,703 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088490   ⟹   XP_038944418
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,371,985 - 62,398,688 (-)NCBI
RefSeq Acc Id: XM_039088491   ⟹   XP_038944419
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,382,081 - 62,391,585 (-)NCBI
RefSeq Acc Id: XR_005491039
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,371,985 - 62,391,590 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_954544   ⟸   NM_199113
- UniProtKB: Q6P722 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766956   ⟸   XM_008768734
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008766955   ⟸   XM_008768733
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453516   ⟸   XM_017598027
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071721   ⟸   ENSRNOT00000087892
RefSeq Acc Id: XP_038944418   ⟸   XM_039088490
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944419   ⟸   XM_039088491
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000087674   ⟸   ENSRNOT00000095198

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P722-F1-model_v2 AlphaFold Q6P722 1-368 view protein structure

Transcriptome

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

Promoters
RGD ID:13698167
Promoter ID:EPDNEW_R8691
Type:single initiation site
Name:Popdc2_1
Description:popeye domain containing 2
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_6.01164,952,697 - 64,952,757EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735226 AgrOrtholog
BioCyc Gene G2FUF-21270 BioCyc
Ensembl Genes ENSRNOG00000058752 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071721 ENTREZGENE
  ENSRNOP00000071721.1 UniProtKB/TrEMBL
  ENSRNOP00000087674.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000087892 ENTREZGENE
  ENSRNOT00000087892.2 UniProtKB/TrEMBL
  ENSRNOT00000095198.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5599130 IMAGE-MGC_LOAD
InterPro cNMP_bd-like UniProtKB/TrEMBL
  Popeye_prot UniProtKB/TrEMBL
  RmlC-like_jellyroll UniProtKB/TrEMBL
KEGG Report rno:360718 UniProtKB/TrEMBL
MGC_CLONE MGC:72601 IMAGE-MGC_LOAD
NCBI Gene 360718 ENTREZGENE
PANTHER Popeye UniProtKB/TrEMBL
Pfam Popeye UniProtKB/TrEMBL
PhenoGen Popdc2 PhenoGen
Superfamily-SCOP cNMP_binding UniProtKB/TrEMBL
UniProt A0A8I6GG90_RAT UniProtKB/TrEMBL
  Q6P722 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Popdc2  popeye domain containing 2  LOC100910206  popeye domain-containing protein 2-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100910206  popeye domain-containing protein 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Popdc2  popeye domain containing 2      Symbol and Name status set to approved 1299863 APPROVED