Ptchd3 (patched domain containing 3) - Rat Genome Database

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Gene: Ptchd3 (patched domain containing 3) Rattus norvegicus
Analyze
Symbol: Ptchd3
Name: patched domain containing 3
RGD ID: 1590039
Description: Located in sperm midpiece. Orthologous to human PTCHD3 (patched domain containing 3 (gene/pseudogene)); INTERACTS WITH bisphenol A; 1,2-dimethylhydrazine (ortholog); 4,4'-sulfonyldiphenol (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: patched domain-containing protein 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810107,594,881 - 107,606,842 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl10107,595,809 - 107,606,834 (+)EnsemblGRCr8
mRatBN7.210107,097,551 - 107,108,575 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10107,097,483 - 107,108,496 (+)EnsemblmRatBN7.2
Rnor_6.010111,031,490 - 111,042,545 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10111,031,414 - 111,042,549 (+)Ensemblrn6Rnor6.0
Rnor_5.010110,607,255 - 110,618,274 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera10105,632,445 - 105,643,506 (+)NCBICelera
Cytogenetic Map10q32.3NCBI
JBrowse:




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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Male germ cell-specific expression of a novel Patched-domain containing gene Ptchd3. Fan J, etal., Biochem Biophys Res Commun. 2007 Nov 23;363(3):757-61. doi: 10.1016/j.bbrc.2007.09.047. Epub 2007 Sep 21.
2. 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.
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ptchd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810107,594,881 - 107,606,842 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl10107,595,809 - 107,606,834 (+)EnsemblGRCr8
mRatBN7.210107,097,551 - 107,108,575 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10107,097,483 - 107,108,496 (+)EnsemblmRatBN7.2
Rnor_6.010111,031,490 - 111,042,545 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10111,031,414 - 111,042,549 (+)Ensemblrn6Rnor6.0
Rnor_5.010110,607,255 - 110,618,274 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera10105,632,445 - 105,643,506 (+)NCBICelera
Cytogenetic Map10q32.3NCBI
PTCHD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381027,397,121 - 27,414,347 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1027,397,121 - 27,414,368 (-)Ensemblhg38GRCh38
GRCh371027,686,050 - 27,703,276 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361027,727,206 - 27,743,227 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1027,450,702 - 27,466,988 (-)NCBICelera
Cytogenetic Map10p12.1NCBI
HuRef1027,403,974 - 27,420,261 (-)NCBIHuRef
CHM1_11027,687,059 - 27,703,249 (-)NCBICHM1_1
T2T-CHM13v2.01027,427,292 - 27,444,622 (-)NCBIT2T-CHM13v2.0
Ptchd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911121,721,050 - 121,734,259 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11121,721,073 - 121,734,249 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm3811121,830,218 - 121,843,438 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11121,830,247 - 121,843,423 (+)Ensemblmm10GRCm38
MGSCv3711121,691,532 - 121,704,752 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3611121,646,337 - 121,659,981 (+)NCBIMGSCv36mm8
Celera11133,565,863 - 133,579,083 (+)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1187.9NCBI
Ptchd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547611,871,133 - 11,896,688 (-)Ensembl
ChiLan1.0NW_00495547611,870,822 - 11,895,903 (-)NCBIChiLan1.0ChiLan1.0
LOC100986128
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2840,049,540 - 40,069,307 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11040,054,867 - 40,074,634 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01027,532,812 - 27,548,871 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11027,894,716 - 27,910,578 (-)NCBIPanPan1.1PanPan1.1panPan2
LOC100685877
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.126,171,232 - 6,182,256 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha25,295,914 - 5,333,729 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
Ptchd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244093447,264,017 - 7,279,202 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366131,814,805 - 1,829,209 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366131,814,805 - 1,851,094 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC110255686
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1042,986,327 - 43,004,688 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11042,987,147 - 43,003,096 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PTCHD3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1926,952,607 - 26,970,565 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl926,953,347 - 26,969,833 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605132,972,692 - 32,989,143 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ptchd3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1962,193,256 - 62,204,277 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:20
Count of miRNA genes:19
Interacting mature miRNAs:20
Transcripts:ENSRNOT00000074372
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1065390777107713808Rat
8657410Bp374Blood pressure QTL 374heart left ventricle size trait (VT:0002753)heart left ventricle end-diastolic diameter (CMO:0000982)1067476608107713808Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063719161107713808Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
12903252Cm113Cardiac mass QTL 1130.047heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068920187107713808Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1064939013107713808Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)1065307813107713808Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076951790107713808Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1073599825107713808Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1089039175107713808Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070698731107713808Rat
12903269Am15Aortic mass QTL 150.042aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
12903266Cm114Cardiac mass QTL 1140.02heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1066817119107713808Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087807758107713808Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1076128947107713808Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091727883107713808Rat
11565453Kidm58Kidney mass QTL 580.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
2301405Cm69Cardiac mass QTL 690.031heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat


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
15 4 15 82 36 32 11 31 11 6 178 68 10 63 81 88 21 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000074372   ⟹   ENSRNOP00000063978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl10107,595,809 - 107,606,834 (+)Ensembl
mRatBN7.2 Ensembl10107,097,483 - 107,108,496 (+)Ensembl
Rnor_6.0 Ensembl10111,031,414 - 111,042,549 (+)Ensembl
RefSeq Acc Id: NM_001408928   ⟹   NP_001395857
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,595,812 - 107,606,836 (+)NCBI
mRatBN7.210107,097,551 - 107,108,575 (+)NCBI
RefSeq Acc Id: XM_039087576   ⟹   XP_038943504
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,595,735 - 107,601,110 (+)NCBI
mRatBN7.210107,098,527 - 107,108,562 (+)NCBI
RefSeq Acc Id: XM_039087577   ⟹   XP_038943505
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,597,758 - 107,606,842 (+)NCBI
mRatBN7.210107,098,669 - 107,108,562 (+)NCBI
RefSeq Acc Id: XM_063269876   ⟹   XP_063125946
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,595,731 - 107,606,842 (+)NCBI
RefSeq Acc Id: XM_063269877   ⟹   XP_063125947
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,595,727 - 107,604,875 (+)NCBI
RefSeq Acc Id: XR_010055255
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,594,881 - 107,601,110 (+)NCBI
RefSeq Acc Id: XR_010055256
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,594,881 - 107,601,108 (+)NCBI
RefSeq Acc Id: XR_010055257
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,595,735 - 107,601,113 (+)NCBI
Ensembl Acc Id: ENSRNOP00000063978   ⟸   ENSRNOT00000074372
RefSeq Acc Id: XP_038943504   ⟸   XM_039087576
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038943505   ⟸   XM_039087577
- Peptide Label: isoform X2
- UniProtKB: A6HLQ5 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001395857   ⟸   NM_001408928
- UniProtKB: M0R3Q7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063125947   ⟸   XM_063269877
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063125946   ⟸   XM_063269876
- Peptide Label: isoform X1
Protein Domains
SSD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R3Q7-F1-model_v2 AlphaFold M0R3Q7 1-905 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590039 AgrOrtholog
BioCyc Gene G2FUF-22347 BioCyc
Ensembl Genes ENSRNOG00000046946 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000074372 ENTREZGENE
  ENSRNOT00000074372.3 UniProtKB/Swiss-Prot
Gene3D-CATH Multidrug efflux transporter AcrB transmembrane domain UniProtKB/Swiss-Prot
InterPro Patched_domain-protein UniProtKB/Swiss-Prot
  Ptc/Disp UniProtKB/Swiss-Prot
  SSD UniProtKB/Swiss-Prot
NCBI Gene 688333 ENTREZGENE
PANTHER PATCHED DOMAIN-CONTAINING PROTEIN 3 UniProtKB/Swiss-Prot
  PATCHED-RELATED UniProtKB/Swiss-Prot
Pfam Patched UniProtKB/Swiss-Prot
PhenoGen Ptchd3 PhenoGen
PROSITE SSD UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000046946 RatGTEx
Superfamily-SCOP Multidrug efflux transporter AcrB transmembrane domain UniProtKB/Swiss-Prot
UniProt A6HLQ5 ENTREZGENE, UniProtKB/TrEMBL
  M0R3Q7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-20 Ptchd3  patched domain containing 3      Symbol and Name status set to provisional 70820 PROVISIONAL