Pfdn5 (prefoldin subunit 5) - Rat Genome Database

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Gene: Pfdn5 (prefoldin subunit 5) Rattus norvegicus
Analyze
Symbol: Pfdn5
Name: prefoldin subunit 5
RGD ID: 1311436
Description: Predicted to enable amyloid-beta binding activity and unfolded protein binding activity. Predicted to be involved in several processes, including negative regulation of canonical Wnt signaling pathway; negative regulation of macromolecule metabolic process; and protein-containing complex assembly. Predicted to act upstream of or within retina development in camera-type eye. Predicted to be located in cytosol and intermediate filament cytoskeleton. Predicted to be part of prefoldin complex. Predicted to be active in cytoplasm. Orthologous to human PFDN5 (prefoldin subunit 5); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC300257; prefoldin 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87135,330,364 - 135,335,102 (+)NCBIGRCr8
mRatBN7.27133,451,778 - 133,456,516 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7133,451,453 - 133,456,516 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,212,778 - 135,217,515 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07137,442,158 - 137,446,895 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07137,427,322 - 137,432,043 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07143,924,662 - 143,929,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7143,924,662 - 143,929,397 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07141,720,703 - 141,725,442 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,075,469 - 141,080,207 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17141,151,896 - 141,156,640 (+)NCBI
Celera7129,885,186 - 129,889,924 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles. Topalidou I, etal., PLoS Genet. 2016 May 18;12(5):e1006074. doi: 10.1371/journal.pgen.1006074. eCollection 2016 May.
Additional References at PubMed
PMID:8889548   PMID:12477932   PMID:15277470   PMID:18281035   PMID:21052544   PMID:31505169  


Genomics

Comparative Map Data
Pfdn5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87135,330,364 - 135,335,102 (+)NCBIGRCr8
mRatBN7.27133,451,778 - 133,456,516 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7133,451,453 - 133,456,516 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,212,778 - 135,217,515 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07137,442,158 - 137,446,895 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07137,427,322 - 137,432,043 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07143,924,662 - 143,929,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7143,924,662 - 143,929,397 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07141,720,703 - 141,725,442 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,075,469 - 141,080,207 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17141,151,896 - 141,156,640 (+)NCBI
Celera7129,885,186 - 129,889,924 (+)NCBICelera
Cytogenetic Map7q36NCBI
PFDN5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381253,295,542 - 53,299,450 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1253,295,291 - 53,299,452 (+)EnsemblGRCh38hg38GRCh38
GRCh371253,689,326 - 53,693,234 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361251,975,502 - 51,979,501 (+)NCBINCBI36Build 36hg18NCBI36
Build 341251,975,583 - 51,979,499NCBI
Celera1253,338,519 - 53,342,520 (+)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1250,730,741 - 50,734,757 (+)NCBIHuRef
CHM1_11253,655,676 - 53,659,674 (+)NCBICHM1_1
T2T-CHM13v2.01253,261,253 - 53,265,162 (+)NCBIT2T-CHM13v2.0
Pfdn5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,234,551 - 102,239,925 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,234,551 - 102,240,308 (+)EnsemblGRCm39 Ensembl
GRCm3815102,326,116 - 102,331,490 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,326,116 - 102,331,873 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,156,547 - 102,161,921 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,154,207 - 102,159,524 (+)NCBIMGSCv36mm8
Celera15104,483,173 - 104,488,550 (+)NCBICelera
Cytogenetic Map15F2NCBI
cM Map1557.48NCBI
Pfdn5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955458555,971 - 559,927 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955458555,971 - 559,927 (+)NCBIChiLan1.0ChiLan1.0
PFDN5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21040,886,410 - 40,890,398 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11240,883,175 - 40,887,118 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01235,454,680 - 35,458,667 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11236,235,552 - 36,239,706 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1236,235,552 - 36,239,706 (-)Ensemblpanpan1.1panPan2
PFDN5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,906,133 - 1,909,613 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,906,133 - 1,909,613 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,339,679 - 44,343,149 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,910,594 - 1,914,080 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,910,594 - 1,914,080 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,928,914 - 1,932,377 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,913,828 - 1,917,308 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02744,740,367 - 44,743,847 (+)NCBIUU_Cfam_GSD_1.0
Pfdn5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494562,581,355 - 62,585,151 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651210,579,635 - 10,599,554 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651210,579,657 - 10,583,477 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PFDN5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11149,407,855 - 49,410,680 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1149,407,761 - 49,411,598 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037196,651,830 - 196,656,242 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pfdn5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249041,332,579 - 1,337,795 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249041,332,518 - 1,336,266 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pfdn5
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:45
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000017794
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat

Markers in Region
BF407910  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27133,450,688 - 133,450,825 (+)MAPPERmRatBN7.2
Rnor_6.07143,923,573 - 143,923,709NCBIRnor6.0
Rnor_5.07141,719,614 - 141,719,750UniSTSRnor5.0
RGSC_v3.47141,074,380 - 141,074,516UniSTSRGSC3.4
Celera7129,884,097 - 129,884,233UniSTS
RH 3.4 Map71065.0UniSTS
Cytogenetic Map7q36UniSTS


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 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017794   ⟹   ENSRNOP00000017794
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,451,778 - 133,456,513 (+)Ensembl
Rnor_6.0 Ensembl7143,924,662 - 143,929,397 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109593   ⟹   ENSRNOP00000077663
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,451,778 - 133,456,513 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000120166   ⟹   ENSRNOP00000087002
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,451,453 - 133,456,516 (+)Ensembl
RefSeq Acc Id: NM_001106794   ⟹   NP_001100264
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87135,330,364 - 135,335,102 (+)NCBI
mRatBN7.27133,451,778 - 133,456,516 (+)NCBI
Rnor_6.07143,924,662 - 143,929,400 (+)NCBI
Rnor_5.07141,720,703 - 141,725,442 (+)NCBI
RGSC_v3.47141,075,469 - 141,080,207 (+)RGD
Celera7129,885,186 - 129,889,924 (+)RGD
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001100264   ⟸   NM_001106794
- UniProtKB: B5DFN4 (UniProtKB/TrEMBL),   F7FF81 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017794   ⟸   ENSRNOT00000017794
RefSeq Acc Id: ENSRNOP00000077663   ⟸   ENSRNOT00000109593
RefSeq Acc Id: ENSRNOP00000087002   ⟸   ENSRNOT00000120166

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5DFN4-F1-model_v2 AlphaFold B5DFN4 1-154 view protein structure

Transcriptome

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

Promoters
RGD ID:13695696
Promoter ID:EPDNEW_R6221
Type:multiple initiation site
Name:Pfdn5_1
Description:prefoldin subunit 5
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_6.07143,924,696 - 143,924,756EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311436 AgrOrtholog
BioCyc Gene G2FUF-31941 BioCyc
Ensembl Genes ENSRNOG00000012985 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017794 ENTREZGENE
  ENSRNOT00000017794.6 UniProtKB/TrEMBL
  ENSRNOT00000109593.1 UniProtKB/TrEMBL
  ENSRNOT00000120166.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.370 UniProtKB/TrEMBL
InterPro PFD_alpha UniProtKB/TrEMBL
  PFD_alpha-like UniProtKB/TrEMBL
  Prefoldin UniProtKB/TrEMBL
KEGG Report rno:300257 UniProtKB/TrEMBL
NCBI Gene 300257 ENTREZGENE
PANTHER PREFOLDIN SUBUNIT 5 UniProtKB/TrEMBL
  PTHR12674 UniProtKB/TrEMBL
Pfam Prefoldin UniProtKB/TrEMBL
PhenoGen Pfdn5 PhenoGen
RatGTEx ENSRNOG00000012985 RatGTEx
Superfamily-SCOP Prefoldin UniProtKB/TrEMBL
UniProt A0A8I5Y1V4_RAT UniProtKB/TrEMBL
  A0A8I6A3H8_RAT UniProtKB/TrEMBL
  A6KCU5_RAT UniProtKB/TrEMBL
  B5DFN4 ENTREZGENE, UniProtKB/TrEMBL
  F7FF81 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-02-26 Pfdn5  prefoldin subunit 5  Pfdn5  prefoldin 5   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pfdn5  prefoldin 5   Pfdn5_predicted  prefoldin 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pfdn5_predicted  prefoldin 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED