Ptcd1 (pentatricopeptide repeat domain 1) - Rat Genome Database

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Gene: Ptcd1 (pentatricopeptide repeat domain 1) Rattus norvegicus
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Symbol: Ptcd1
Name: pentatricopeptide repeat domain 1
RGD ID: 1311473
Description: Predicted to enable tRNA binding activity. Predicted to be involved in tRNA 3'-end processing. Located in mitochondrial matrix. Orthologous to several human genes including PTCD1 (pentatricopeptide repeat domain 1); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether (ortholog); acrylamide (ortholog); bis(2-ethylhexyl) phthalate (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC304278; pentatricopeptide repeat-containing protein 1, mitochondrial
RGD Orthologs
Human
Dog
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81214,559,419 - 14,577,198 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1214,559,368 - 14,577,198 (+)EnsemblGRCr8
mRatBN7.2129,445,656 - 9,463,434 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl129,445,714 - 9,463,508 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1210,250,866 - 10,268,460 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01210,874,072 - 10,891,666 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0129,897,496 - 9,915,090 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01211,215,795 - 11,233,633 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1211,215,886 - 11,233,633 (+)Ensemblrn6Rnor6.0
Rnor_5.01213,284,898 - 13,302,736 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4129,759,859 - 9,777,602 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1211,251,048 - 11,268,669 (+)NCBICelera
RGSC_v3.1129,791,843 - 9,806,612 (+)NCBI
Cytogenetic Map12p11NCBI
JBrowse:




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

Biological Process

Cellular Component
mitochondrial matrix  (IBA,IDA,IEA)
mitochondrion  (IEA)

Molecular Function
rRNA binding  (IEA)
tRNA binding  (IBA,IEA,ISS)

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. Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells. Rackham O, etal., Nucleic Acids Res. 2009 Sep;37(17):5859-67. doi: 10.1093/nar/gkp627. Epub 2009 Aug 3.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:29617655  


Genomics

Comparative Map Data
Ptcd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81214,559,419 - 14,577,198 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1214,559,368 - 14,577,198 (+)EnsemblGRCr8
mRatBN7.2129,445,656 - 9,463,434 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl129,445,714 - 9,463,508 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1210,250,866 - 10,268,460 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01210,874,072 - 10,891,666 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0129,897,496 - 9,915,090 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01211,215,795 - 11,233,633 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1211,215,886 - 11,233,633 (+)Ensemblrn6Rnor6.0
Rnor_5.01213,284,898 - 13,302,736 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4129,759,859 - 9,777,602 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1211,251,048 - 11,268,669 (+)NCBICelera
RGSC_v3.1129,791,843 - 9,806,612 (+)NCBI
Cytogenetic Map12p11NCBI
ATP5MF-PTCD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38799,416,739 - 99,466,167 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl799,419,749 - 99,466,197 (-)Ensemblhg38GRCh38
GRCh37799,014,362 - 99,063,790 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map7q22.1NCBI
HuRef793,650,105 - 93,700,497 (-)NCBIHuRef
CHM1_1798,944,440 - 98,993,924 (-)NCBICHM1_1
T2T-CHM13v2.07100,655,640 - 100,705,074 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2798,374,136 - 98,423,596 (-)NCBI
ATP5J2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1610,128,623 - 10,172,377 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha611,739,951 - 11,797,945 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0610,114,826 - 10,172,592 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl610,129,341 - 10,136,537 (+)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl1550,115,464 - 50,115,730 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.169,983,666 - 10,041,345 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.069,963,388 - 10,021,039 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0610,197,131 - 10,254,872 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
PTCD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl36,360,732 - 6,371,382 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.136,360,713 - 6,374,180 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.236,679,488 - 6,694,114 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in Ptcd1
94 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:135
Count of miRNA genes:100
Interacting mature miRNAs:115
Transcripts:ENSRNOT00000060924
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
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12592191825247790Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121120049452308831Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)12129775522Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
1357337Gluco3Glucose level QTL 30.0004adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)12116966671Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12348941648489416Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)12138687564Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049752308831Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12133700600Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)121174352852308831Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)121186960016966542Rat
61334Gluco17Glucose level QTL 176.3adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)12116966671Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)12138635130Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12128133365Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)121223300030490641Rat
1300174Bw15Body weight QTL 152.93body mass (VT:0001259)body weight loss (CMO:0001399)12128606299Rat
1331787Rf41Renal function QTL 412.998kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)12133700556Rat
724526Uae3Urinary albumin excretion QTL 34.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)12115486827Rat
1331763Wbc2White blood cell count QTL 23.162leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)121120049452308831Rat
7204484Bp358Blood pressure QTL 3580.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12124849755Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)61120049452308831Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12141361854Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12274769447747694Rat
2303568Bw88Body weight QTL 883body mass (VT:0001259)body weight (CMO:0000012)12128606299Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12308718048087180Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12563330650633306Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12790162533938215Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat

Markers in Region
D12Wox3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,454,135 - 9,454,231 (+)MAPPERmRatBN7.2
Rnor_6.01211,224,261 - 11,224,356NCBIRnor6.0
Rnor_5.01213,293,364 - 13,293,459UniSTSRnor5.0
RGSC_v3.4129,768,226 - 9,768,321UniSTSRGSC3.4
Celera1211,259,293 - 11,259,388UniSTS
RGSC_v3.1129,798,153 - 9,798,249RGD
Cytogenetic Map12p11UniSTS
RH138815  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,449,327 - 9,449,454 (+)MAPPERmRatBN7.2
Rnor_6.01211,219,453 - 11,219,579NCBIRnor6.0
Rnor_5.01213,288,556 - 13,288,682UniSTSRnor5.0
RGSC_v3.4129,763,418 - 9,763,544UniSTSRGSC3.4
Celera1211,254,485 - 11,254,611UniSTS
RH 3.4 Map12112.8UniSTS
Cytogenetic Map12p11UniSTS
BI298983  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,463,074 - 9,463,234 (+)MAPPERmRatBN7.2
Rnor_6.01211,233,200 - 11,233,359NCBIRnor6.0
Rnor_5.01213,302,303 - 13,302,462UniSTSRnor5.0
RGSC_v3.4129,777,169 - 9,777,328UniSTSRGSC3.4
Celera1211,268,236 - 11,268,395UniSTS
RH 3.4 Map12101.68UniSTS
Cytogenetic Map12p11UniSTS


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 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000060924   ⟹   ENSRNOP00000057644
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1214,559,368 - 14,577,198 (+)Ensembl
mRatBN7.2 Ensembl129,445,768 - 9,463,508 (+)Ensembl
Rnor_6.0 Ensembl1211,215,893 - 11,233,633 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076896   ⟹   ENSRNOP00000068093
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1214,559,467 - 14,577,197 (+)Ensembl
mRatBN7.2 Ensembl129,445,714 - 9,463,432 (+)Ensembl
Rnor_6.0 Ensembl1211,215,886 - 11,233,561 (+)Ensembl
RefSeq Acc Id: NM_001401119   ⟹   NP_001388048
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81214,559,473 - 14,577,198 (+)NCBI
mRatBN7.2129,445,709 - 9,463,434 (+)NCBI
RefSeq Acc Id: XM_006248873   ⟹   XP_006248935
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81214,559,419 - 14,577,198 (+)NCBI
mRatBN7.2129,445,656 - 9,463,434 (+)NCBI
Rnor_6.01211,215,795 - 11,233,559 (+)NCBI
Rnor_5.01213,284,898 - 13,302,736 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039089342   ⟹   XP_038945270
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81214,559,590 - 14,577,198 (+)NCBI
mRatBN7.2129,445,776 - 9,463,434 (+)NCBI
RefSeq Acc Id: XM_039089343   ⟹   XP_038945271
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81214,561,879 - 14,577,198 (+)NCBI
mRatBN7.2129,448,107 - 9,463,434 (+)NCBI
RefSeq Acc Id: XM_039089344   ⟹   XP_038945272
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81214,559,420 - 14,577,198 (+)NCBI
mRatBN7.2129,445,656 - 9,463,434 (+)NCBI
RefSeq Acc Id: XP_006248935   ⟸   XM_006248873
- Peptide Label: isoform X2
- UniProtKB: A6K1F1 (UniProtKB/TrEMBL),   D4AA10 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000057644   ⟸   ENSRNOT00000060924
Ensembl Acc Id: ENSRNOP00000068093   ⟸   ENSRNOT00000076896
RefSeq Acc Id: XP_038945272   ⟸   XM_039089344
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038945270   ⟸   XM_039089342
- Peptide Label: isoform X1
- UniProtKB: A2VD13 (UniProtKB/Swiss-Prot),   A6K1F1 (UniProtKB/TrEMBL),   D4AA10 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038945271   ⟸   XM_039089343
- Peptide Label: isoform X3
RefSeq Acc Id: NP_001388048   ⟸   NM_001401119
- UniProtKB: A2VD13 (UniProtKB/Swiss-Prot),   A6K1F1 (UniProtKB/TrEMBL),   D4AA10 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A2VD13-F1-model_v2 AlphaFold A2VD13 1-686 view protein structure

Transcriptome

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

Promoters
RGD ID:13698425
Promoter ID:EPDNEW_R8940
Type:initiation region
Name:Ptcd1_1
Description:pentatricopeptide repeat domain 1
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_6.01211,215,875 - 11,215,935EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311473 AgrOrtholog
BioCyc Gene G2FUF-20058 BioCyc
Ensembl Genes ENSRNOG00000000987 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000060924 ENTREZGENE
  ENSRNOT00000076896 ENTREZGENE
  ENSRNOT00000076896.3 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7113830 IMAGE-MGC_LOAD
InterPro Pentatricopeptide_repeat UniProtKB/Swiss-Prot
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot
MGC_CLONE MGC:156763 IMAGE-MGC_LOAD
NCBI Gene 304278 ENTREZGENE
PANTHER 2-OXOGLUTARATE AND IRON-DEPENDENT OXYGENASE DOMAIN-CONTAINING PROTEIN 2 UniProtKB/Swiss-Prot
  PENTATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 1, MITOCHONDRIAL UniProtKB/Swiss-Prot
Pfam PPR_2 UniProtKB/Swiss-Prot
  PPR_3 UniProtKB/Swiss-Prot
PhenoGen Ptcd1 PhenoGen
PROSITE PPR UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000000987 RatGTEx
UniProt A2VD13 ENTREZGENE
  A6K1F1 ENTREZGENE, UniProtKB/TrEMBL
  D4AA10 ENTREZGENE, UniProtKB/TrEMBL
  PTCD1_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ptcd1  pentatricopeptide repeat domain 1   Ptcd1_predicted  pentatricopeptide repeat domain 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ptcd1_predicted  pentatricopeptide repeat domain 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED