Ptcd2 (pentatricopeptide repeat domain 2) - Rat Genome Database

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Gene: Ptcd2 (pentatricopeptide repeat domain 2) Mus musculus
Analyze
Symbol: Ptcd2
Name: pentatricopeptide repeat domain 2
RGD ID: 1321138
MGI Page MGI
Description: Acts upstream of or within several processes, including liver development; regulation of mRNA processing; and ventricular cardiac muscle tissue morphogenesis. Located in mitochondrion. Is expressed in central nervous system and sensory organ. Orthologous to human PTCD2 (pentatricopeptide repeat domain 2).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 1190005P08Rik; pentatricopeptide repeat-containing protein 2; pentatricopeptide repeat-containing protein 2, mitochondrial
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391399,456,157 - 99,481,215 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1399,456,155 - 99,481,213 (-)EnsemblGRCm39 Ensembl
GRCm381399,319,649 - 99,344,678 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1399,319,647 - 99,344,705 (-)EnsemblGRCm38mm10GRCm38
MGSCv3713100,089,604 - 100,114,633 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3613100,419,806 - 100,444,835 (-)NCBIMGSCv36mm8
Celera13102,971,896 - 102,996,749 (-)NCBICelera
Cytogenetic Map13D1NCBI
cM Map1352.76NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
mitochondrion  (HDA,IBA,ISO)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. Mouse MP Annotation Import Pipeline RGD automated import pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Database resources of the National Center for Biotechnology Information. Wheeler DL, etal., Nucleic Acids Res 2001 Jan 1;29(1):11-6.
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10512203   PMID:10922068   PMID:11042159   PMID:11076861   PMID:12477932   PMID:12520002   PMID:14610273   PMID:15840001   PMID:16033648   PMID:16141072  
PMID:16141073   PMID:18614015   PMID:18729827   PMID:18799693   PMID:21873635   PMID:34133714   PMID:36114006  


Genomics

Comparative Map Data
Ptcd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391399,456,157 - 99,481,215 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1399,456,155 - 99,481,213 (-)EnsemblGRCm39 Ensembl
GRCm381399,319,649 - 99,344,678 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1399,319,647 - 99,344,705 (-)EnsemblGRCm38mm10GRCm38
MGSCv3713100,089,604 - 100,114,633 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3613100,419,806 - 100,444,835 (-)NCBIMGSCv36mm8
Celera13102,971,896 - 102,996,749 (-)NCBICelera
Cytogenetic Map13D1NCBI
cM Map1352.76NCBI
PTCD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38572,320,373 - 72,368,395 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl572,320,367 - 72,368,395 (+)EnsemblGRCh38hg38GRCh38
GRCh37571,616,200 - 71,664,222 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36571,651,956 - 71,690,936 (+)NCBINCBI36Build 36hg18NCBI36
Build 34571,651,973 - 71,691,792NCBI
Celera567,511,586 - 67,550,568 (+)NCBICelera
Cytogenetic Map5q13.2NCBI
HuRef566,821,949 - 66,860,941 (+)NCBIHuRef
CHM1_1571,048,875 - 71,087,855 (+)NCBICHM1_1
T2T-CHM13v2.0572,801,543 - 72,849,569 (+)NCBIT2T-CHM13v2.0
Ptcd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8232,446,441 - 32,474,114 (-)NCBIGRCr8
mRatBN7.2230,712,276 - 30,739,968 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl230,712,280 - 30,739,942 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx237,782,104 - 37,809,729 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0235,876,429 - 35,904,060 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0230,680,625 - 30,708,291 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0229,570,581 - 29,598,328 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl229,570,538 - 29,598,277 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0248,732,573 - 48,760,245 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4230,310,431 - 30,338,099 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1230,231,255 - 30,258,441 (-)NCBI
Celera226,737,451 - 26,765,119 (-)NCBICelera
Cytogenetic Map2q12NCBI
Ptcd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555751,126,639 - 1,158,181 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555751,126,978 - 1,156,727 (+)NCBIChiLan1.0ChiLan1.0
PTCD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2442,955,057 - 42,993,686 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1541,108,761 - 41,147,314 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0542,953,639 - 42,992,301 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1543,552,528 - 43,591,161 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl543,552,528 - 43,591,162 (-)Ensemblpanpan1.1panPan2
PTCD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1255,351,678 - 55,382,881 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl255,351,558 - 55,382,746 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha252,320,030 - 52,351,013 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0255,867,971 - 55,898,984 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl255,867,859 - 55,898,818 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1252,928,162 - 52,959,182 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0253,696,288 - 53,727,283 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0254,586,965 - 54,617,985 (+)NCBIUU_Cfam_GSD_1.0
Ptcd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213186,693,878 - 186,723,121 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365494,135,811 - 4,165,009 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365494,135,854 - 4,164,991 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTCD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1648,605,012 - 48,636,181 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11648,605,014 - 48,635,954 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21652,593,553 - 52,620,277 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTCD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1466,658,183 - 66,695,339 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl466,658,212 - 66,699,405 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604915,414,598 - 15,455,658 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ptcd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249051,427,530 - 1,453,796 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249051,427,508 - 1,454,418 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ptcd2
787 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:187
Count of miRNA genes:159
Interacting mature miRNAs:169
Transcripts:ENSMUST00000022153
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142147Mvwf4_mmodifier of von Willebrand factor 4 (mouse)Not determined20477612112898424Mouse
4142314Tailaq3_mtail length adjusted QTL 3 (mouse)Not determined55720354112431103Mouse
4140959W10q17_mweight 10 weeks QTL 17 (mouse)Not determined55720354112431103Mouse
4141992W6q16_mweight 6 weeks QTL 16 (mouse)Not determined55720354112431103Mouse
4142241Tailq3_mtail length QTL 3 (mouse)Not determined55720354112431103Mouse
10402414Sgp5_mserum gp70 production 5 (mouse)Not determined1356470456105422186Mouse
1301445Listr2_mlisteriosis resistance 2 (mouse)Not determined1366744601100744746Mouse
1301593Heal8_mwound healing/regeneration 8 (mouse)Not determined1368053999102054119Mouse
14696726Kidrq3_mkidney weight, right QTL 3 (mouse)1368217066102217066Mouse
14747007Mancz11_mmandible centroid size 11 (mouse)1370111284104111284Mouse
4141266Mol3_mmodifier of LPS-response 3 (mouse)Not determined76132600112431103Mouse
12880414V125Dq10_mvitamin D active form serum level QTL 10 (mouse)1378036508112036508Mouse
10043997Bw40_mbody weight QTL 40 (mouse)Not determined1479239045113239162Mouse
10045623Heal18_mwound healing regeneration 18 (mouse)Not determined1379239045113239162Mouse
1558741Ses10_msalmonella enteritidis susceptibility 10 (mouse)Not determined1382739968116740106Mouse
4142465Pbwg17_mpostnatal body weight growth 17 (mouse)Not determined1383876060117876256Mouse
14700691Cisaq1_mcoxsackieviral infection serum ALT QTL 1 (mouse)1386148119120461536Mouse
4140995Fbtq6_mfemoral bone trait QTL 6 (mouse)Not determined1386341617120341758Mouse
4141728Egaq4_mearly growth adjusted QTL 4 (mouse)Not determined87901985112431103Mouse
1300939Hrtfm6_mheart failure modifier 6 (mouse)Not determined1391383692120883175Mouse
1300876Tanidd2_mtally ho associated non-insulin dependednt diabetes mellitus 2 (mouse)Not determined1391965303120883175Mouse
1301142Heal2_mwound healing/regeneration 2 (mouse)Not determined1393875267120883175Mouse
4142338Skmw18_mskeletal muscle weight 18 (mouse)Not determined1394528399120883175Mouse
1558763Gct9_mgranulosa cell tumorigenesis 9 (mouse)Not determined1395036824120883175Mouse
1357468Rplag_mreduced platelet aggregation (mouse)Not determined1395502130120883175Mouse
14746974Manh75_mmandible shape 75 (mouse)1399386647120883175Mouse

Markers in Region
Ptcd2  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map13D1UniSTS
cM Map13 UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000022153   ⟹   ENSMUSP00000022153
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1399,456,155 - 99,481,213 (-)Ensembl
GRCm38.p6 Ensembl1399,319,647 - 99,344,705 (-)Ensembl
RefSeq Acc Id: NM_026873   ⟹   NP_081149
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391399,456,157 - 99,481,186 (-)NCBI
GRCm381399,319,649 - 99,344,678 (-)ENTREZGENE
MGSCv3713100,089,604 - 100,114,633 (-)RGD
Celera13102,971,896 - 102,996,749 (-)RGD
cM Map13 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_036158153   ⟹   XP_036014046
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391399,463,227 - 99,481,215 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_081149 (Get FASTA)   NCBI Sequence Viewer  
  XP_036014046 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH16563 (Get FASTA)   NCBI Sequence Viewer  
  AAH25110 (Get FASTA)   NCBI Sequence Viewer  
  BAB23336 (Get FASTA)   NCBI Sequence Viewer  
  EDL00835 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000022153
  ENSMUSP00000022153.7
GenBank Protein Q8R3K3 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_081149   ⟸   NM_026873
- UniProtKB: Q91VG3 (UniProtKB/Swiss-Prot),   Q9D0S7 (UniProtKB/Swiss-Prot),   Q8R3K3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000022153   ⟸   ENSMUST00000022153
RefSeq Acc Id: XP_036014046   ⟸   XM_036158153
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8R3K3-F1-model_v2 AlphaFold Q8R3K3 1-381 view protein structure

Promoters
RGD ID:8681136
Promoter ID:EPDNEW_M18599
Type:initiation region
Name:Ptcd2_1
Description:Mus musculus pentatricopeptide repeat domain 2 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381399,344,698 - 99,344,758EPDNEW
RGD ID:6824276
Promoter ID:MM_KWN:15045
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000052249,   NM_026873
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3613100,113,961 - 100,114,827 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1916177 AgrOrtholog
Ensembl Genes ENSMUSG00000021650 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000022153 ENTREZGENE
  ENSMUST00000022153.8 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot
InterPro MRPS27/PTCD2 UniProtKB/Swiss-Prot
  Pentatricopeptide_repeat UniProtKB/Swiss-Prot
  PTCD2 UniProtKB/Swiss-Prot
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot
KEGG Report mmu:68927 UniProtKB/Swiss-Prot
MGD MGI:1916177 ENTREZGENE
NCBI Gene 68927 ENTREZGENE
PANTHER PENTATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 2, MITOCHONDRIAL UniProtKB/Swiss-Prot
  PTHR14700 UniProtKB/Swiss-Prot
Pfam MRP-S27 UniProtKB/Swiss-Prot
PhenoGen Ptcd2 PhenoGen
PROSITE PPR UniProtKB/Swiss-Prot
UniProt PTCD2_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q91VG3 ENTREZGENE
  Q9D0S7 ENTREZGENE
UniProt Secondary Q91VG3 UniProtKB/Swiss-Prot
  Q9D0S7 UniProtKB/Swiss-Prot