Pdcl3 (phosducin-like 3) - Rat Genome Database

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Gene: Pdcl3 (phosducin-like 3) Rattus norvegicus
Analyze
Symbol: Pdcl3
Name: phosducin-like 3
RGD ID: 1309663
Description: Enables protein folding chaperone. Involved in cellular response to heat and protein folding. Predicted to be located in cytosol; endoplasmic reticulum; and nuclear lumen. Predicted to be part of protein-containing complex. Predicted to be active in cytoplasm. Orthologous to human PDCL3 (phosducin like 3); INTERACTS WITH 2,6-dinitrotoluene; 2-methoxyethanol; 5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC316348; MGC116329; phosducin-like 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
mRatBN7.2941,234,322 - 41,243,769 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl941,234,234 - 41,243,735 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx949,728,486 - 49,736,952 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0954,851,230 - 54,859,696 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0953,135,081 - 53,143,552 (+)NCBIRnor_WKY
Rnor_6.0945,672,257 - 45,680,728 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl945,672,157 - 45,680,799 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0945,362,541 - 45,371,012 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4938,004,222 - 38,012,693 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1938,005,635 - 38,014,107 (+)NCBI
Celera938,984,793 - 38,993,264 (+)NCBICelera
Cytogenetic Map9q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. Interaction of a Novel Chaperone PhLP2A With the Heat Shock Protein Hsp90. Krzemień-Ojak Ł, etal., J Cell Biochem. 2017 Feb;118(2):420-429. doi: 10.1002/jcb.25669. Epub 2016 Oct 17.
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
Additional References at PubMed
PMID:12477932   PMID:15371430   PMID:15489334   PMID:17429077   PMID:23792958   PMID:26059764  


Genomics

Comparative Map Data
Pdcl3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2941,234,322 - 41,243,769 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl941,234,234 - 41,243,735 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx949,728,486 - 49,736,952 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0954,851,230 - 54,859,696 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0953,135,081 - 53,143,552 (+)NCBIRnor_WKY
Rnor_6.0945,672,257 - 45,680,728 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl945,672,157 - 45,680,799 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0945,362,541 - 45,371,012 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4938,004,222 - 38,012,693 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1938,005,635 - 38,014,107 (+)NCBI
Celera938,984,793 - 38,993,264 (+)NCBICelera
Cytogenetic Map9q22NCBI
PDCL3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382100,562,993 - 100,576,739 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2100,562,993 - 100,576,739 (+)EnsemblGRCh38hg38GRCh38
GRCh372101,179,455 - 101,193,201 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362100,545,859 - 100,559,633 (+)NCBINCBI36Build 36hg18NCBI36
Build 342100,637,944 - 100,651,719NCBI
Celera295,384,039 - 95,397,821 (+)NCBICelera
Cytogenetic Map2q11.2NCBI
HuRef294,943,898 - 94,957,677 (+)NCBIHuRef
CHM1_12101,183,727 - 101,197,486 (+)NCBICHM1_1
T2T-CHM13v2.02101,021,740 - 101,035,465 (+)NCBIT2T-CHM13v2.0
Pdcl3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39139,026,895 - 39,036,317 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl139,024,689 - 39,036,319 (+)EnsemblGRCm39 Ensembl
GRCm38138,987,814 - 38,997,236 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl138,985,608 - 38,997,238 (+)EnsemblGRCm38mm10GRCm38
MGSCv37139,044,659 - 39,054,081 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36138,932,360 - 38,941,782 (+)NCBIMGSCv36mm8
Celera138,777,037 - 38,786,281 (+)NCBICelera
Cytogenetic Map1BNCBI
Pdcl3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554706,553,450 - 6,563,814 (+)NCBIChiLan1.0ChiLan1.0
PDCL3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A101,538,872 - 101,551,669 (+)NCBIpanpan1.1PanPan1.1panPan2
PDCL3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11042,214,127 - 42,223,986 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1042,215,120 - 42,223,906 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1042,137,411 - 42,147,413 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01043,080,268 - 43,090,236 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1043,079,573 - 43,090,129 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11042,791,342 - 42,801,288 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01043,075,653 - 43,085,591 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01043,266,979 - 43,276,929 (-)NCBIUU_Cfam_GSD_1.0
Pdcl3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629286,141,438 - 86,150,373 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936661419,113 - 428,032 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDCL3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl353,674,509 - 53,692,928 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1353,681,798 - 53,693,034 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2356,244,971 - 56,256,183 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDCL3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1144,275,182 - 4,289,041 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041171,892,827 - 171,907,083 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdcl3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247495,410,476 - 5,422,533 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247495,410,501 - 5,419,625 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pdcl3
40 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:247
Count of miRNA genes:167
Interacting mature miRNAs:193
Transcripts:ENSRNOT00000017882
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
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92043051965430519Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92207120067071200Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)92213332249968732Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92375402458157242Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92375402461381613Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)92746863972468639Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)93696235977814038Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat

Markers in Region
RH128453  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2941,241,884 - 41,242,103 (+)MAPPERmRatBN7.2
Rnor_6.0945,679,820 - 45,680,038NCBIRnor6.0
Rnor_5.0945,370,104 - 45,370,322UniSTSRnor5.0
RGSC_v3.4938,011,785 - 38,012,003UniSTSRGSC3.4
Celera938,992,356 - 38,992,574UniSTS
RH 3.4 Map9382.2UniSTS
Cytogenetic Map9q21UniSTS
RH133234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2941,242,385 - 41,242,588 (+)MAPPERmRatBN7.2
Rnor_6.0945,680,321 - 45,680,523NCBIRnor6.0
Rnor_5.0945,370,605 - 45,370,807UniSTSRnor5.0
RGSC_v3.4938,012,286 - 38,012,488UniSTSRGSC3.4
Celera938,992,857 - 38,993,059UniSTS
Cytogenetic Map9q21UniSTS
RH141636  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2941,243,453 - 41,243,672 (+)MAPPERmRatBN7.2
Rnor_6.0945,681,389 - 45,681,607NCBIRnor6.0
Rnor_5.0945,371,673 - 45,371,891UniSTSRnor5.0
RGSC_v3.4938,013,354 - 38,013,572UniSTSRGSC3.4
Celera938,993,925 - 38,994,143UniSTS
RH 3.4 Map9380.99UniSTS
Cytogenetic Map9q21UniSTS


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 53 37 19 37 8 11 74 35 34 11 8
Low 4 4 4 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017882   ⟹   ENSRNOP00000017882
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl941,234,234 - 41,243,735 (+)Ensembl
Rnor_6.0 Ensembl945,672,157 - 45,680,799 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102761   ⟹   ENSRNOP00000096257
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl941,237,153 - 41,243,689 (+)Ensembl
RefSeq Acc Id: NM_001025709   ⟹   NP_001020880
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2941,234,322 - 41,242,793 (+)NCBI
Rnor_6.0945,672,257 - 45,680,728 (+)NCBI
Rnor_5.0945,362,541 - 45,371,012 (+)NCBI
RGSC_v3.4938,004,222 - 38,012,693 (+)RGD
Celera938,984,793 - 38,993,264 (+)RGD
Sequence:
RefSeq Acc Id: XM_039083581   ⟹   XP_038939509
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2941,234,593 - 41,243,769 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001020880 (Get FASTA)   NCBI Sequence Viewer  
  XP_038939509 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99162 (Get FASTA)   NCBI Sequence Viewer  
  EDL99204 (Get FASTA)   NCBI Sequence Viewer  
  EDL99205 (Get FASTA)   NCBI Sequence Viewer  
  Q4KLJ8 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001020880   ⟸   NM_001025709
- UniProtKB: Q4KLJ8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017882   ⟸   ENSRNOT00000017882
RefSeq Acc Id: XP_038939509   ⟸   XM_039083581
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000096257   ⟸   ENSRNOT00000102761
Protein Domains
Phosducin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4KLJ8-F1-model_v2 AlphaFold Q4KLJ8 1-240 view protein structure

Transcriptome

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

Promoters
RGD ID:13696623
Promoter ID:EPDNEW_R7147
Type:initiation region
Name:Pdcl3_1
Description:phosducin-like 3
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_6.0945,672,265 - 45,672,325EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309663 AgrOrtholog
BioCyc Gene G2FUF-27759 BioCyc
Ensembl Genes ENSRNOG00000013286 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017882 ENTREZGENE
  ENSRNOP00000017882.5 UniProtKB/TrEMBL
  ENSRNOP00000096257.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017882 ENTREZGENE
  ENSRNOT00000017882.7 UniProtKB/TrEMBL
  ENSRNOT00000102761.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7381935 IMAGE-MGC_LOAD
InterPro Phosducin_thioredoxin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:316348 UniProtKB/Swiss-Prot
MGC_CLONE MGC:116329 IMAGE-MGC_LOAD
NCBI Gene 316348 ENTREZGENE
Pfam Phosducin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pdcl3 PhenoGen
Superfamily-SCOP SSF52833 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AQA2_RAT UniProtKB/TrEMBL
  A0A8L2Q950_RAT UniProtKB/TrEMBL
  PDCL3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Pdcl3  phosducin-like 3  Pdcl3_predicted  phosducin-like 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Pdcl3_predicted  phosducin-like 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED