Pdf (peptide deformylase (mitochondrial)) - Rat Genome Database

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Gene: Pdf (peptide deformylase (mitochondrial)) Rattus norvegicus
Analyze
Symbol: Pdf
Name: peptide deformylase (mitochondrial)
RGD ID: 1582894
Description: Predicted to enable peptide deformylase activity. Predicted to be involved in peptidyl-methionine modification; positive regulation of cell population proliferation; and post-translational protein modification. Predicted to be active in mitochondrion. Orthologous to human PDF (peptide deformylase, mitochondrial); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; fipronil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC690214; peptide deformylase, mitochondrial; peptide deformylase-like protein-like; similar to peptide deformylase-like protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81951,859,159 - 51,861,281 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1951,859,159 - 51,861,281 (-)EnsemblGRCr8
mRatBN7.21934,949,408 - 34,951,621 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,948,256 - 34,951,515 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1941,764,887 - 41,767,009 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01942,418,234 - 42,420,356 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01944,717,520 - 44,719,642 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd1945,646,447 - 45,648,569 (-)NCBIDahl_SR_JrHsd
Lyon_Normotensive1943,771,312 - 43,773,434 (-)NCBILyon_Normotensive
Lyon_Hypertensive1945,644,666 - 45,646,788 (-)NCBILyon_Hypertensive
F344_StmMcwi1943,400,347 - 43,402,469 (-)NCBIF344_StmMcwi
Rnor_6.01939,244,242 - 39,246,636 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1939,245,212 - 39,246,545 (-)Ensemblrn6Rnor6.0
Rnor_5.01950,107,811 - 50,109,999 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41936,902,288 - 36,904,128 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1934,372,756 - 34,375,150 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse:




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

Biological Process

Cellular Component
mitochondrion  (IBA,IEA,ISO)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15489958  


Genomics

Comparative Map Data
Pdf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81951,859,159 - 51,861,281 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1951,859,159 - 51,861,281 (-)EnsemblGRCr8
mRatBN7.21934,949,408 - 34,951,621 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,948,256 - 34,951,515 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1941,764,887 - 41,767,009 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01942,418,234 - 42,420,356 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01944,717,520 - 44,719,642 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd1945,646,447 - 45,648,569 (-)NCBIDahl_SR_JrHsd
Lyon_Normotensive1943,771,312 - 43,773,434 (-)NCBILyon_Normotensive
Lyon_Hypertensive1945,644,666 - 45,646,788 (-)NCBILyon_Hypertensive
F344_StmMcwi1943,400,347 - 43,402,469 (-)NCBIF344_StmMcwi
Rnor_6.01939,244,242 - 39,246,636 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1939,245,212 - 39,246,545 (-)Ensemblrn6Rnor6.0
Rnor_5.01950,107,811 - 50,109,999 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41936,902,288 - 36,904,128 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1934,372,756 - 34,375,150 (-)NCBICelera
Cytogenetic Map19q12NCBI
PDF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381669,326,913 - 69,330,588 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1669,326,913 - 69,330,588 (-)Ensemblhg38GRCh38
GRCh371669,360,816 - 69,364,491 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361667,920,025 - 67,921,999 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1653,877,064 - 53,879,038 (-)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1655,240,685 - 55,242,659 (-)NCBIHuRef
CHM1_11670,770,526 - 70,772,500 (-)NCBICHM1_1
T2T-CHM13v2.01675,128,608 - 75,132,285 (-)NCBIT2T-CHM13v2.0
Pdf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398107,772,921 - 107,775,246 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8107,771,330 - 107,775,246 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388107,046,289 - 107,048,614 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8107,044,698 - 107,048,614 (-)Ensemblmm10GRCm38
MGSCv378109,570,189 - 109,572,514 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
Celera8111,272,839 - 111,275,163 (-)NCBICelera
Cytogenetic Map8D3NCBI
cM Map853.55NCBI
Pdf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554847,363,861 - 7,366,159 (+)Ensembl
ChiLan1.0NW_0049554847,363,861 - 7,366,159 (+)NCBIChiLan1.0ChiLan1.0
PDF
(Pan paniscus - bonobo/pygmy chimpanzee)		 No map positions available.
PDF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1580,323,573 - 80,325,665 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
PDF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl617,652,356 - 17,654,740 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1617,652,297 - 17,658,257 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2616,599,145 - 16,602,410 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pdf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474617,041,374 - 17,043,966 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474617,041,370 - 17,043,985 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pdf
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11726,771,168 - 26,772,926 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pdf
38 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:36
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000036634
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19799775052997750Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)194072709254856850Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)194072709254856850Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)194072709254856850Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 91 59 6 355 191 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000036634   ⟹   ENSRNOP00000036742
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1951,859,159 - 51,861,281 (-)Ensembl
mRatBN7.2 Ensembl1934,948,256 - 34,951,515 (-)Ensembl
Rnor_6.0 Ensembl1939,245,212 - 39,246,545 (-)Ensembl
RefSeq Acc Id: NM_001401071   ⟹   NP_001388000
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81951,859,159 - 51,861,281 (-)NCBI
mRatBN7.21934,949,408 - 34,951,530 (-)NCBI
Dahl_SR_JrHsd1945,646,447 - 45,648,569 (-)NCBI
Lyon_Normotensive1943,771,312 - 43,773,434 (-)NCBI
Lyon_Hypertensive1945,644,666 - 45,646,788 (-)NCBI
F344_StmMcwi1943,400,347 - 43,402,469 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001388000 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000036742
  ENSRNOP00000036742.5
Ensembl Acc Id: ENSRNOP00000036742   ⟸   ENSRNOT00000036634
RefSeq Acc Id: NP_001388000   ⟸   NM_001401071
- Peptide Label: precursor
- UniProtKB: F1LVY9 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LVY9-F1-model_v2 AlphaFold F1LVY9 1-231 view protein structure

Transcriptome

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

Promoters
RGD ID:13701127
Promoter ID:EPDNEW_R11642
Type:multiple initiation site
Name:Pdf_1
Description:peptide deformylase
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_6.01939,246,552 - 39,246,612EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1582894 AgrOrtholog
BioCyc Gene G2FUF-5767 BioCyc
Ensembl Genes ENSRNOG00000022303 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036634 ENTREZGENE
  ENSRNOT00000036634.7 UniProtKB/TrEMBL
Gene3D-CATH 3.90.45.10 UniProtKB/TrEMBL
InterPro Peptide_deformylase UniProtKB/TrEMBL
  Peptide_deformylase_sf UniProtKB/TrEMBL
NCBI Gene 690214 ENTREZGENE
PANTHER PEPTIDE DEFORMYLASE, MITOCHONDRIAL UniProtKB/TrEMBL
  PTHR10458 UniProtKB/TrEMBL
Pfam Pep_deformylase UniProtKB/TrEMBL
PhenoGen Pdf PhenoGen
PIRSF Pep_def UniProtKB/TrEMBL
PRINTS PDEFORMYLASE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022303 RatGTEx
Superfamily-SCOP Fmet_deformylase UniProtKB/TrEMBL
UniProt F1LVY9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Pdf  peptide deformylase (mitochondrial)  LOC100363967  peptide deformylase-like protein-like  Data merged from RGD:2321990 1643240 APPROVED
2012-10-02 Pdf  peptide deformylase (mitochondrial)  LOC690214  similar to peptide deformylase-like protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100363967  peptide deformylase-like protein-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-01-09 LOC690214  similar to peptide deformylase-like protein  LOC686957  similar to peptide deformylase-like protein  Data merged from RGD:1591264 1643240 APPROVED
2006-11-20 LOC686957  similar to peptide deformylase-like protein      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC690214  similar to peptide deformylase-like protein      Symbol and Name status set to provisional 70820 PROVISIONAL