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 co-translational protein modification and positive regulation of cell population proliferation. 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
Dog
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81951,859,159 - 51,861,281 (-)NCBIGRCr8
mRatBN7.21934,949,408 - 34,951,621 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,948,256 - 34,951,515 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1941,764,887 - 41,767,009 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01942,418,234 - 42,420,356 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01944,717,520 - 44,719,642 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01939,244,242 - 39,246,636 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1939,245,212 - 39,246,545 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01950,107,811 - 50,109,999 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41936,902,288 - 36,904,128 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1934,372,756 - 34,375,150 (-)NCBICelera
Cytogenetic Map19q12NCBI
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

Biological Process

Cellular Component
mitochondrion  (IBA,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 (-)NCBIGRCr8
mRatBN7.21934,949,408 - 34,951,621 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1934,948,256 - 34,951,515 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1941,764,887 - 41,767,009 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01942,418,234 - 42,420,356 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01944,717,520 - 44,719,642 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01939,244,242 - 39,246,636 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1939,245,212 - 39,246,545 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01950,107,811 - 50,109,999 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41936,902,288 - 36,904,128 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (-)EnsemblGRCh38hg38GRCh38
GRCh371669,360,816 - 69,364,491 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361667,920,025 - 67,921,999 (-)NCBINCBI36Build 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 Ensembl
GRCm388107,046,289 - 107,048,614 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8107,044,698 - 107,048,614 (-)EnsemblGRCm38mm10GRCm38
MGSCv378109,570,189 - 109,572,514 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554847,363,861 - 7,366,159 (+)NCBIChiLan1.0ChiLan1.0
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474617,041,370 - 17,043,985 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pdf
4 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)192753020737947399Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
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)19136824771Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)192753020737947399Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)192753020737947399Rat


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 3 6 65 35 33 11 3
Low 4 4 4 5 5 9 8 5
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000036634   ⟹   ENSRNOP00000036742
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
Protein Sequences
Protein RefSeqs NP_001388000 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000036742
  ENSRNOP00000036742.5
RefSeq 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
  ENSRNOT00000036634.6 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