Ptchd4 (patched domain containing 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ptchd4 (patched domain containing 4) Rattus norvegicus
Analyze
Symbol: Ptchd4
Name: patched domain containing 4
RGD ID: 1563020
Description: Predicted to be active in membrane. Orthologous to human PTCHD4 (patched domain containing 4); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC301271; patched domain-containing protein 4; RGD1563020; similar to OTTHUMP00000016566
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8925,951,395 - 26,163,296 (-)NCBIGRCr8
mRatBN7.2918,462,934 - 18,666,272 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl918,463,737 - 18,665,705 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0921,137,150 - 21,339,398 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl921,141,077 - 21,338,582 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0920,001,317 - 20,202,955 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4914,220,416 - 14,424,280 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera916,162,302 - 16,367,307 (-)NCBICelera
Cytogenetic Map9q13NCBI
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
membrane  (IBA)

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ptchd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8925,951,395 - 26,163,296 (-)NCBIGRCr8
mRatBN7.2918,462,934 - 18,666,272 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl918,463,737 - 18,665,705 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0921,137,150 - 21,339,398 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl921,141,077 - 21,338,582 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0920,001,317 - 20,202,955 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4914,220,416 - 14,424,280 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera916,162,302 - 16,367,307 (-)NCBICelera
Cytogenetic Map9q13NCBI
PTCHD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38647,856,673 - 48,111,197 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl647,856,673 - 48,111,197 (-)EnsemblGRCh38hg38GRCh38
GRCh37647,824,409 - 48,078,933 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36647,953,998 - 48,144,384 (-)NCBINCBI36Build 36hg18NCBI36
Celera649,402,015 - 49,592,692 (-)NCBICelera
Cytogenetic Map6p12.3NCBI
HuRef647,573,689 - 47,763,951 (-)NCBIHuRef
CHM1_1647,848,697 - 48,039,382 (-)NCBICHM1_1
T2T-CHM13v2.0647,698,467 - 47,952,968 (-)NCBIT2T-CHM13v2.0
Ptchd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391742,626,646 - 43,004,339 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1742,626,838 - 42,815,968 (+)EnsemblGRCm39 Ensembl
GRCm381742,315,851 - 42,507,742 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1742,315,947 - 42,505,077 (+)EnsemblGRCm38mm10GRCm38
MGSCv371742,452,896 - 42,644,690 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361741,317,589 - 41,507,471 (+)NCBIMGSCv36mm8
MGSCv361741,780,176 - 41,971,225 (+)NCBIMGSCv36mm8
Celera1745,720,241 - 45,918,575 (+)NCBICelera
Cytogenetic Map17B3NCBI
cM Map1719.65NCBI
Ptchd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543712,254,176 - 12,423,871 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543712,253,731 - 12,423,865 (-)NCBIChiLan1.0ChiLan1.0
PTCHD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2562,369,575 - 62,607,535 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1658,235,720 - 58,473,613 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0647,440,981 - 47,652,718 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1648,724,043 - 48,915,518 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl648,724,318 - 48,916,307 (-)Ensemblpanpan1.1panPan2
PTCHD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11215,910,253 - 16,094,827 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1215,916,840 - 16,095,556 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1216,007,216 - 16,060,826 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01216,543,805 - 16,597,465 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11216,063,763 - 16,117,369 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01216,146,821 - 16,200,403 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01216,292,916 - 16,346,683 (-)NCBIUU_Cfam_GSD_1.0
Ptchd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494651,274,358 - 51,456,893 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647612,503,474 - 12,676,577 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647612,503,324 - 12,678,204 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTCHD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl742,570,094 - 42,770,225 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1742,570,100 - 42,770,035 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PTCHD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11724,216,587 - 24,413,202 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1724,217,389 - 24,412,311 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604447,893,154 - 48,091,257 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ptchd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475413,079,430 - 13,255,076 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475413,079,762 - 13,270,656 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ptchd4
1173 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:40
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000016940
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9795472022071169Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91696139840594091Rat


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

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system appendage
High
Medium
Low 64 2 1
Below cutoff 1 1 1 1 4 4 8 12 16 4

Sequence


RefSeq Acc Id: ENSRNOT00000016940   ⟹   ENSRNOP00000016940
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl918,463,737 - 18,665,373 (-)Ensembl
Rnor_6.0 Ensembl921,141,077 - 21,338,582 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118927   ⟹   ENSRNOP00000094067
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl918,463,737 - 18,665,705 (-)Ensembl
RefSeq Acc Id: XM_008766914   ⟹   XP_008765136
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8925,951,395 - 26,163,296 (-)NCBI
mRatBN7.2918,462,934 - 18,666,272 (-)NCBI
Rnor_6.0921,137,150 - 21,339,398 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766916   ⟹   XP_008765138
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8925,951,395 - 26,162,592 (-)NCBI
mRatBN7.2918,462,934 - 18,665,373 (-)NCBI
Rnor_6.0921,137,150 - 21,338,607 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596760   ⟹   XP_017452249
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8925,951,395 - 26,162,592 (-)NCBI
mRatBN7.2918,462,934 - 18,665,373 (-)NCBI
Rnor_6.0921,137,150 - 21,338,607 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_008765136 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765138 (Get FASTA)   NCBI Sequence Viewer  
  XP_017452249 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016940.6
  ENSRNOP00000094067.1
RefSeq Acc Id: XP_008765136   ⟸   XM_008766914
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008765138   ⟸   XM_008766916
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017452249   ⟸   XM_017596760
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000016940   ⟸   ENSRNOT00000016940
RefSeq Acc Id: ENSRNOP00000094067   ⟸   ENSRNOT00000118927
Protein Domains
SSD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRK8-F1-model_v2 AlphaFold D3ZRK8 1-904 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:1563020 AgrOrtholog
BioCyc Gene G2FUF-28091 BioCyc
Ensembl Genes ENSRNOG00000012708 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016940.7 UniProtKB/TrEMBL
  ENSRNOT00000118927.1 UniProtKB/TrEMBL
Gene3D-CATH Multidrug efflux transporter AcrB transmembrane domain UniProtKB/TrEMBL
InterPro Patched UniProtKB/TrEMBL
  SSD_5TM UniProtKB/TrEMBL
KEGG Report rno:301271 UniProtKB/TrEMBL
NCBI Gene 301271 ENTREZGENE
PANTHER PATCHED DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
  PATCHED-RELATED UniProtKB/TrEMBL
Pfam Patched UniProtKB/TrEMBL
PhenoGen Ptchd4 PhenoGen
PROSITE SSD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012708 RatGTEx
Superfamily-SCOP Multidrug efflux transporter AcrB transmembrane domain UniProtKB/TrEMBL
UniProt A0A8I6AYQ0_RAT UniProtKB/TrEMBL
  D3ZRK8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-12 Ptchd4  patched domain containing 4  RGD1563020  similar to OTTHUMP00000016566  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563020  similar to OTTHUMP00000016566   RGD1563020_predicted  similar to OTTHUMP00000016566 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563020_predicted  similar to OTTHUMP00000016566 (predicted)  LOC301271  similar to OTTHUMP00000016566  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC301271  similar to OTTHUMP00000016566      Symbol and Name status set to provisional 70820 PROVISIONAL