Ptcd1 (pentatricopeptide repeat domain 1) - Rat Genome Database

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Gene: Ptcd1 (pentatricopeptide repeat domain 1) Rattus norvegicus
Analyze
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); bisphenol A (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC304278; pentatricopeptide repeat-containing protein 1, mitochondrial
RGD Orthologs
Human
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81214,559,419 - 14,577,198 (+)NCBIGRCr8
mRatBN7.2129,445,656 - 9,463,434 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl129,445,714 - 9,463,508 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1210,250,866 - 10,268,460 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01210,874,072 - 10,891,666 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0129,897,496 - 9,915,090 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01211,215,795 - 11,233,633 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1211,215,886 - 11,233,633 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01213,284,898 - 13,302,736 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4129,759,859 - 9,777,602 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1129,791,843 - 9,806,612 (+)NCBI
Celera1211,251,048 - 11,268,669 (+)NCBICelera
Cytogenetic Map12p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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)

Molecular Function
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 (+)NCBIGRCr8
mRatBN7.2129,445,656 - 9,463,434 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl129,445,714 - 9,463,508 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1210,250,866 - 10,268,460 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01210,874,072 - 10,891,666 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0129,897,496 - 9,915,090 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01211,215,795 - 11,233,633 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1211,215,886 - 11,233,633 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01213,284,898 - 13,302,736 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4129,759,859 - 9,777,602 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1129,791,843 - 9,806,612 (+)NCBI
Celera1211,251,048 - 11,268,669 (+)NCBICelera
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 (-)EnsemblGRCh38hg38GRCh38
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_Tasha
ROS_Cfam_1.0610,114,826 - 10,172,592 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl610,129,341 - 10,136,537 (+)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_1.0
PTCD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl36,360,732 - 6,371,382 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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
83 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
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)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449846669029Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449546669029Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
724526Uae3Urinary albumin excretion QTL 34.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)12390696910373166Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12683319017870186Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)12931821612829686Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat

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
RGSC_v3.1129,798,153 - 9,798,249RGD
Celera1211,259,293 - 11,259,388UniSTS
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
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 1 22 22 12 12 12 65 33 34 9
Low 2 21 35 29 7 29 8 11 9 2 7 2 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000060924   ⟹   ENSRNOP00000057644
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,445,768 - 9,463,508 (+)Ensembl
Rnor_6.0 Ensembl1211,215,893 - 11,233,633 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076896   ⟹   ENSRNOP00000068093
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
RefSeq Acc Id: ENSRNOP00000057644   ⟸   ENSRNOT00000060924
RefSeq 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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060924.4 UniProtKB/TrEMBL
  ENSRNOT00000076896 ENTREZGENE
  ENSRNOT00000076896.3 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7113830 IMAGE-MGC_LOAD
InterPro Pentatricopeptide_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:304278 UniProtKB/TrEMBL
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, UniProtKB/TrEMBL
  PENTATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 1, MITOCHONDRIAL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PPR_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PPR_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ptcd1 PhenoGen
PROSITE PPR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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