Ptchd1 (patched domain containing 1) - Rat Genome Database

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Gene: Ptchd1 (patched domain containing 1) Rattus norvegicus
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Symbol: Ptchd1
Name: patched domain containing 1
RGD ID: 1564527
Description: Predicted to be involved in several processes, including smoothened signaling pathway; social behavior; and thalamus development. Predicted to act upstream of or within chemical synaptic transmission and memory. Predicted to be located in dendritic spine. Predicted to be active in plasma membrane and synapse. Human ortholog(s) of this gene implicated in autistic disorder. Orthologous to human PTCHD1 (patched domain containing 1); INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC317517; patched domain-containing protein 1; RGD1564527; similar to patched domain containing 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X43,496,907 - 43,548,413 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX43,496,907 - 43,548,544 (+)EnsemblGRCr8
mRatBN7.2X39,681,910 - 39,733,416 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX39,681,910 - 39,733,519 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX40,905,386 - 40,956,900 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X44,372,699 - 44,424,207 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X42,057,286 - 42,108,794 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X42,558,912 - 42,610,430 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX42,558,931 - 42,614,242 (+)Ensemblrn6Rnor6.0
Rnor_5.0X42,866,040 - 42,917,474 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X61,079,670 - 61,131,155 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX40,277,508 - 40,329,013 (+)NCBICelera
Cytogenetic MapXq21NCBI
JBrowse:




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

Biological Process

Cellular Component
dendritic spine  (IEA,ISO)
membrane  (IEA)
plasma membrane  (IBA,IEA,ISO)
synapse  (IBA,IEA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
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
Additional References at PubMed
PMID:20844286   PMID:27007844   PMID:29118110  


Genomics

Comparative Map Data
Ptchd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X43,496,907 - 43,548,413 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX43,496,907 - 43,548,544 (+)EnsemblGRCr8
mRatBN7.2X39,681,910 - 39,733,416 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX39,681,910 - 39,733,519 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX40,905,386 - 40,956,900 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X44,372,699 - 44,424,207 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X42,057,286 - 42,108,794 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X42,558,912 - 42,610,430 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX42,558,931 - 42,614,242 (+)Ensemblrn6Rnor6.0
Rnor_5.0X42,866,040 - 42,917,474 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X61,079,670 - 61,131,155 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX40,277,508 - 40,329,013 (+)NCBICelera
Cytogenetic MapXq21NCBI
PTCHD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X23,334,396 - 23,404,374 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX23,334,318 - 23,404,374 (+)Ensemblhg38GRCh38
GRCh37X23,352,966 - 23,422,491 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X23,262,906 - 23,324,839 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X23,112,751 - 23,172,076NCBI
CeleraX27,474,669 - 27,536,553 (+)NCBICelera
Cytogenetic MapXp22.11NCBI
HuRefX21,094,048 - 21,155,060 (+)NCBIHuRef
CHM1_1X23,384,049 - 23,445,953 (+)NCBICHM1_1
T2T-CHM13v2.0X22,917,921 - 22,987,936 (+)NCBIT2T-CHM13v2.0
Ptchd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X154,352,732 - 154,407,185 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX154,356,451 - 154,406,810 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X155,569,736 - 155,624,170 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX155,573,455 - 155,623,814 (-)Ensemblmm10GRCm38
MGSCv37X152,004,279 - 152,057,870 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X150,914,257 - 150,964,043 (-)NCBIMGSCv36mm8
CeleraX138,872,944 - 138,926,972 (-)NCBICelera
Cytogenetic MapXF3NCBI
cM MapX72.38NCBI
Ptchd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555093,715,771 - 3,767,541 (+)Ensembl
ChiLan1.0NW_0049555093,716,086 - 3,767,541 (+)NCBIChiLan1.0ChiLan1.0
PTCHD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X25,131,355 - 25,192,568 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X25,134,743 - 25,195,957 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X15,929,619 - 15,991,194 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X23,305,555 - 23,366,273 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX23,305,555 - 23,366,273 (+)EnsemblpanPan2panpan1.1
PTCHD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X19,096,787 - 19,153,367 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX19,096,559 - 19,148,528 (+)EnsemblcanFam3CanFam3.1
ROS_Cfam_1.0X19,050,277 - 19,105,259 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX19,049,225 - 19,101,569 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X19,089,857 - 19,144,818 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X19,119,773 - 19,174,752 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X19,176,247 - 19,231,008 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ptchd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X12,031,839 - 12,087,657 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366241,072,857 - 1,125,994 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366241,072,857 - 1,125,962 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTCHD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX19,507,739 - 19,561,828 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X19,508,501 - 19,563,298 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X20,851,579 - 20,904,599 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTCHD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X21,810,530 - 21,874,109 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX21,810,956 - 21,870,417 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605623,674,097 - 23,736,621 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ptchd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248298,458,628 - 8,512,511 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248298,458,430 - 8,513,011 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ptchd1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X34,543,288 - 34,598,627 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ptchd1
278 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:78
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000044129
Prediction methods:Microtar, Miranda, Pita, 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
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2447036044931007Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X400149344939387Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2447036045082063Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X197044046970440Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X811148653111486Rat


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
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
9 8 52 130 58 54 27 23 27 6 203 95 116 64 79 27 12 12

Sequence


Ensembl Acc Id: ENSRNOT00000044129   ⟹   ENSRNOP00000044293
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX42,558,931 - 42,614,242 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000113700   ⟹   ENSRNOP00000085114
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX43,496,907 - 43,548,544 (+)Ensembl
mRatBN7.2 EnsemblX39,681,910 - 39,733,519 (+)Ensembl
RefSeq Acc Id: NM_001191734   ⟹   NP_001178663
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X43,496,907 - 43,548,413 (+)NCBI
mRatBN7.2X39,681,910 - 39,733,416 (+)NCBI
Rnor_6.0X42,558,912 - 42,610,430 (+)NCBI
Rnor_5.0X42,866,040 - 42,917,474 (+)NCBI
CeleraX40,277,508 - 40,329,013 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178663 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96105 (Get FASTA)   NCBI Sequence Viewer  
  EDL96106 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000085114
  ENSRNOP00000085114.1
RefSeq Acc Id: NP_001178663   ⟸   NM_001191734
- UniProtKB: A0A8I5ZYJ0 (UniProtKB/TrEMBL),   A6IPQ7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000044293   ⟸   ENSRNOT00000044129
Ensembl Acc Id: ENSRNOP00000085114   ⟸   ENSRNOT00000113700
Protein Domains
SSD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZX73-F1-model_v2 AlphaFold D3ZX73 1-783 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:1564527 AgrOrtholog
BioCyc Gene G2FUF-2446 BioCyc
Ensembl Genes ENSRNOG00000003675 Ensembl
  ENSRNOG00000069252 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000113700 ENTREZGENE
  ENSRNOT00000113700.2 UniProtKB/TrEMBL
Gene3D-CATH Multidrug efflux transporter AcrB transmembrane domain UniProtKB/TrEMBL
InterPro Patched_domain-protein UniProtKB/TrEMBL
  Ptc/Disp UniProtKB/TrEMBL
  SSD UniProtKB/TrEMBL
KEGG Report rno:317517 UniProtKB/TrEMBL
NCBI Gene 317517 ENTREZGENE
PANTHER PATCHED DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PATCHED-RELATED UniProtKB/TrEMBL
Pfam Patched UniProtKB/TrEMBL
PhenoGen Ptchd1 PhenoGen
PROSITE SSD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003675 RatGTEx
  ENSRNOG00000069252 RatGTEx
Superfamily-SCOP Multidrug efflux transporter AcrB transmembrane domain UniProtKB/TrEMBL
UniProt A0A8I5ZYJ0 ENTREZGENE, UniProtKB/TrEMBL
  A6IPQ7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ptchd1  patched domain containing 1   Ptchd1_predicted  patched domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ptchd1_predicted  patched domain containing 1 (predicted)  RGD1564527_predicted  similar to patched domain containing 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1564527_predicted  similar to patched domain containing 1 (predicted)  LOC317517  similar to patched domain containing 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317517  similar to patched domain containing 1      Symbol and Name status set to provisional 70820 PROVISIONAL