Pdcl2 (phosducin-like 2) - Rat Genome Database

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Gene: Pdcl2 (phosducin-like 2) Rattus norvegicus
Analyze
Symbol: Pdcl2
Name: phosducin-like 2
RGD ID: 1559712
Description: Predicted to be involved in protein folding and spermatid development. Predicted to act upstream of or within acrosome assembly and sperm axoneme assembly. Predicted to be active in endoplasmic reticulum. Orthologous to human PDCL2 (phosducin like 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; Cuprizon; trichloroethene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC498352; phosducin-like protein 2; RGD1559712; similar to phosducin-like 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81432,228,776 - 32,249,467 (+)NCBIGRCr8
mRatBN7.21431,874,563 - 31,895,265 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1431,874,578 - 31,895,272 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1432,241,106 - 32,261,770 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01433,548,995 - 33,569,668 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01432,034,112 - 32,054,782 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01434,384,338 - 34,404,920 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1434,389,991 - 34,404,883 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01434,170,394 - 34,190,924 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41434,151,347 - 34,166,988 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1431,175,969 - 31,196,319 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Pdcl2Ratcongenital disorder of glycosylation type IIk  ISOPDCL2 (Homo sapiens)8554872ClinVar Annotator: match by term: TMEM165-CDGClinVarPMID:22521416 more ...
Pdcl2Ratgastrointestinal stromal tumor  ISOPDCL2 (Homo sapiens)8554872ClinVar Annotator: match by term: Gastrointestinal stromal tumorClinVarPMID:1279971 more ...
Pdcl2Ratmale infertility  ISOPDCL2 (Homo sapiens)8554872ClinVar Annotator: match by term: Male infertilityClinVar 

1 to 9 of 9 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Pdcl2Rat2,3,7,8-tetrachlorodibenzodioxine increases expressionEXP 6480464Tetrachlorodibenzodioxin results in increased expression of PDCL2 mRNACTDPMID:32109520
Pdcl2Ratbenzo[a]pyrene increases methylationISOPDCL2 (Homo sapiens)6480464Benzo(a)pyrene results in increased methylation of PDCL2 promoterCTDPMID:27901495
Pdcl2Ratbis(2-ethylhexyl) phthalate increases expressionISOPdcl2 (Mus musculus)6480464Diethylhexyl Phthalate results in increased expression of PDCL2 mRNACTDPMID:34319233
Pdcl2RatCuprizon decreases expressionEXP 6480464Cuprizone results in decreased expression of PDCL2 mRNACTDPMID:26577399
Pdcl2Ratepoxiconazole decreases expressionISOPdcl2 (Mus musculus)6480464epoxiconazole results in decreased expression of PDCL2 mRNACTDPMID:35436446
Pdcl2Ratgenistein decreases expressionISOPdcl2 (Mus musculus)6480464Genistein results in decreased expression of PDCL2 mRNACTDPMID:32186404
Pdcl2Ratparacetamol multiple interactionsISOPdcl2 (Mus musculus)6480464MAP3K5 protein affects the reaction [Acetaminophen results in increased expression of PDCL2 mRNA]CTDPMID:18700144
Pdcl2Ratpirinixic acid multiple interactionsISOPDCL2 (Homo sapiens)6480464[pirinixic acid binds to and results in increased activity of PPARA protein] which results in increased expression of PDCL2 mRNACTDPMID:19710929
Pdcl2Rattrichloroethene decreases expressionEXP 6480464Trichloroethylene results in decreased expression of PDCL2 mRNACTDPMID:33387578

1 to 9 of 9 rows

Biological Process
1 to 12 of 12 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Pdcl2Ratacrosome assembly involved_inISOPdcl2 (Mus musculus)1624291 PMID:36278277RGDPMID:36278277
Pdcl2Ratacrosome assembly acts_upstream_of_or_withinIEAUniProtKB:Q78Y63 and ensembl:ENSMUSP000000311451600115GO_REF:0000107EnsemblGO_REF:0000107
Pdcl2Ratacrosome assembly acts_upstream_of_or_withinISOPdcl2 (Mus musculus)1624291MGI:7546801 PMID:36278277RGDPMID:36278277
Pdcl2Ratflagellated sperm motility acts_upstream_of_or_withinISOPdcl2 (Mus musculus)1624291MGI:7546801 PMID:36278277RGDPMID:36278277
Pdcl2Ratflagellated sperm motility acts_upstream_of_or_withinIEAUniProtKB:Q78Y63 and ensembl:ENSMUSP000000311451600115GO_REF:0000107EnsemblGO_REF:0000107
Pdcl2Ratprotein folding involved_inIBAPANTHER:PTN000475349 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Pdcl2Ratsperm axoneme assembly acts_upstream_of_or_withinISOPdcl2 (Mus musculus)1624291MGI:7546801 PMID:36278277RGDPMID:36278277
Pdcl2Ratsperm axoneme assembly acts_upstream_of_or_withinIEAUniProtKB:Q78Y63 and ensembl:ENSMUSP000000311451600115GO_REF:0000107EnsemblGO_REF:0000107
Pdcl2Ratsperm flagellum assembly acts_upstream_of_or_withinIEAUniProtKB:Q78Y63 and ensembl:ENSMUSP000000311451600115GO_REF:0000107EnsemblGO_REF:0000107
Pdcl2Ratsperm flagellum assembly acts_upstream_of_or_withinISOPdcl2 (Mus musculus)1624291MGI:7546801 PMID:36278277RGDPMID:36278277
Pdcl2Ratspermatid development involved_inISOPdcl2 (Mus musculus)1624291 PMID:36253364RGDPMID:36253364
Pdcl2Ratspermatid development involved_inIEAUniProtKB:Q78Y63 and ensembl:ENSMUSP000000311451600115GO_REF:0000107EnsemblGO_REF:0000107
1 to 12 of 12 rows

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Pdcl2Ratcytoplasm is_active_inIBAMGI:1890655 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Pdcl2Ratendoplasmic reticulum located_inISOPdcl2 (Mus musculus)1624291 PMID:36278277RGDPMID:36278277
Pdcl2Ratendoplasmic reticulum is_active_inIEAUniProtKB:Q78Y63 and ensembl:ENSMUSP000000311451600115GO_REF:0000107EnsemblGO_REF:0000107
Pdcl2Ratendoplasmic reticulum is_active_inISOPdcl2 (Mus musculus)1624291 PMID:36278277RGDPMID:36278277


#
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:36462395  



Pdcl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81432,228,776 - 32,249,467 (+)NCBIGRCr8
mRatBN7.21431,874,563 - 31,895,265 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1431,874,578 - 31,895,272 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1432,241,106 - 32,261,770 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01433,548,995 - 33,569,668 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01432,034,112 - 32,054,782 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01434,384,338 - 34,404,920 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1434,389,991 - 34,404,883 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01434,170,394 - 34,190,924 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41434,151,347 - 34,166,988 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1431,175,969 - 31,196,319 (+)NCBICelera
Cytogenetic Map14p11NCBI
PDCL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38455,556,519 - 55,592,245 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl455,556,519 - 55,592,245 (-)EnsemblGRCh38hg38GRCh38
GRCh37456,422,686 - 56,458,412 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36456,117,449 - 56,153,136 (-)NCBINCBI36Build 36hg18NCBI36
Build 34456,263,620 - 56,299,307NCBI
Celera453,924,722 - 53,960,420 (-)NCBICelera
Cytogenetic Map4q12NCBI
HuRef452,371,990 - 52,407,692 (-)NCBIHuRef
CHM1_1456,457,818 - 56,493,430 (-)NCBICHM1_1
T2T-CHM13v2.0459,044,647 - 59,080,385 (-)NCBIT2T-CHM13v2.0
Pdcl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39576,459,963 - 76,479,003 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl576,459,962 - 76,479,003 (-)EnsemblGRCm39 Ensembl
GRCm38576,312,116 - 76,331,156 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl576,312,115 - 76,331,156 (-)EnsemblGRCm38mm10GRCm38
MGSCv37576,741,171 - 76,760,136 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36577,386,921 - 77,405,886 (-)NCBIMGSCv36mm8
Celera573,577,496 - 73,596,447 (-)NCBICelera
Cytogenetic Map5C3.3NCBI
cM Map540.88NCBI
Pdcl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544715,363,806 - 15,386,071 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544715,364,116 - 15,386,071 (+)NCBIChiLan1.0ChiLan1.0
PDCL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2374,200,117 - 74,237,980 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1474,402,121 - 74,439,885 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0468,343,615 - 68,381,364 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1474,907,904 - 74,944,895 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl474,907,904 - 74,944,895 (+)Ensemblpanpan1.1panPan2
PDCL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11347,832,161 - 47,861,716 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1347,832,166 - 47,861,614 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1347,789,247 - 47,813,445 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01348,443,111 - 48,472,648 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1348,443,116 - 48,472,559 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11348,117,888 - 48,147,442 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01347,646,577 - 47,676,403 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01348,595,351 - 48,624,891 (-)NCBIUU_Cfam_GSD_1.0
Pdcl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528528,365,853 - 28,390,522 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648217,907,713 - 17,932,224 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648217,907,713 - 17,927,007 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDCL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl854,917,583 - 54,950,062 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1854,916,145 - 54,950,048 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2858,603,756 - 58,634,863 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDCL2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1712,969,993 - 13,005,120 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl712,978,707 - 13,005,082 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606613,726,839 - 13,761,767 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdcl2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476113,852,491 - 13,899,054 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476113,852,827 - 13,898,718 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

.

.
Variants in Pdcl2
137 total Variants

Predicted Target Of
Summary Value
Count of predictions:18
Count of miRNA genes:17
Interacting mature miRNAs:18
Transcripts:ENSRNOT00000002953
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.


1 to 10 of 16 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat

1 to 10 of 16 rows



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 9 23 105 50 45 20 22 20 2 115 62 89 17 60 25



Ensembl Acc Id: ENSRNOT00000002953   ⟹   ENSRNOP00000002953
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1431,880,161 - 31,895,272 (+)Ensembl
Rnor_6.0 Ensembl1434,389,991 - 34,404,883 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101910   ⟹   ENSRNOP00000097165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1431,874,578 - 31,895,272 (+)Ensembl
RefSeq Acc Id: NM_001399023   ⟹   NP_001385952
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81432,228,776 - 32,249,467 (+)NCBI
mRatBN7.21431,874,563 - 31,895,265 (+)NCBI
Protein RefSeqs NP_001385952 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89907 (Get FASTA)   NCBI Sequence Viewer  
  EDL89908 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002953.3
  ENSRNOP00000097165
  ENSRNOP00000097165.1
GenBank Protein QHI05890 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Acc Id: ENSRNOP00000002953   ⟸   ENSRNOT00000002953
Ensembl Acc Id: ENSRNOP00000097165   ⟸   ENSRNOT00000101910
RefSeq Acc Id: NP_001385952   ⟸   NM_001399023
- UniProtKB: A0A8I6B5E6 (UniProtKB/TrEMBL),   A0A6B9RYC6 (UniProtKB/TrEMBL)
Phosducin thioredoxin-like

Name Modeler Protein Id AA Range Protein Structure
AF-F1M610-F1-model_v2 AlphaFold F1M610 1-239 view protein structure


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



1 to 19 of 19 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-15943 BioCyc
Ensembl Genes ENSRNOG00000002169 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002953.5 UniProtKB/TrEMBL
  ENSRNOT00000101910 ENTREZGENE
  ENSRNOT00000101910.1 UniProtKB/TrEMBL
Gene3D-CATH Glutaredoxin UniProtKB/TrEMBL
InterPro Phosducin-like_chap/apop_reg UniProtKB/TrEMBL
  Phosducin_thioredoxin-like_dom UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/TrEMBL
NCBI Gene 498352 ENTREZGENE
PANTHER PHOSDUCIN-LIKE PROTEIN 2 UniProtKB/TrEMBL
  VIRAL IAP-ASSOCIATED FACTOR HOMOLOG UniProtKB/TrEMBL
Pfam Phosducin UniProtKB/TrEMBL
PhenoGen Pdcl2 PhenoGen
RatGTEx ENSRNOG00000002169 RatGTEx
Superfamily-SCOP Thiordxn-like_fd UniProtKB/TrEMBL
UniProt A0A6B9RYC6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6B5E6 ENTREZGENE, UniProtKB/TrEMBL
  F1M610_RAT UniProtKB/TrEMBL
1 to 19 of 19 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-28 Pdcl2  phosducin-like 2  RGD1559712_predicted  similar to phosducin-like 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559712_predicted  similar to phosducin-like 2 (predicted)  LOC498352  similar to phosducin-like 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498352  similar to phosducin-like 2      Symbol and Name status set to provisional 70820 PROVISIONAL