PTCHD4 (patched domain containing 4) - Rat Genome Database

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Gene: PTCHD4 (patched domain containing 4) Canis lupus familiaris
Analyze
Symbol: PTCHD4
Name: patched domain containing 4
RGD ID: 12307395
Description: ASSOCIATED WITH genetic disease (ortholog); FOUND IN membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: C12H6orf138; patched domain-containing protein 4; patched domain-containing protein C6orf138 homolog
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
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  (IEA)

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
2214 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium
Low 10 12 4
Below cutoff 5 5 12 6 6 6 6 6 8 6 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000003323   ⟹   ENSCAFP00000003086
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1215,916,840 - 16,095,556 (-)Ensembl
RefSeq Acc Id: XM_003639429   ⟹   XP_003639477
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11215,910,253 - 16,094,827 (-)NCBI
Dog10K_Boxer_Tasha1216,007,216 - 16,060,826 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038492011   ⟹   XP_038347939
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11216,063,763 - 16,117,369 (-)NCBI
RefSeq Acc Id: XM_038554270   ⟹   XP_038410198
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01216,292,916 - 16,346,683 (-)NCBI
RefSeq Acc Id: XM_038618137   ⟹   XP_038474065
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01216,146,821 - 16,200,403 (-)NCBI
RefSeq Acc Id: XM_038683726   ⟹   XP_038539654
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01216,543,805 - 16,597,465 (-)NCBI
Protein Sequences
Protein RefSeqs XP_003639477 (Get FASTA)   NCBI Sequence Viewer  
  XP_038347939 (Get FASTA)   NCBI Sequence Viewer  
  XP_038410198 (Get FASTA)   NCBI Sequence Viewer  
  XP_038474065 (Get FASTA)   NCBI Sequence Viewer  
  XP_038539654 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCAFP00000003086.4
Reference Protein Sequences
RefSeq Acc Id: XP_003639477   ⟸   XM_003639429
- Sequence:
RefSeq Acc Id: ENSCAFP00000003086   ⟸   ENSCAFT00000003323
RefSeq Acc Id: XP_038347939   ⟸   XM_038492011
RefSeq Acc Id: XP_038474065   ⟸   XM_038618137
RefSeq Acc Id: XP_038539654   ⟸   XM_038683726
RefSeq Acc Id: XP_038410198   ⟸   XM_038554270
Protein Domains
SSD


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000002100 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000003323.5 UniProtKB/TrEMBL
Gene3D-CATH Multidrug efflux transporter AcrB transmembrane domain UniProtKB/TrEMBL
InterPro Ptc/Disp UniProtKB/TrEMBL
  SSD UniProtKB/TrEMBL
NCBI Gene PTCHD4 ENTREZGENE
PANTHER PATCHED DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
  PATCHED-RELATED UniProtKB/TrEMBL
Pfam Patched UniProtKB/TrEMBL
PROSITE SSD UniProtKB/TrEMBL
Superfamily-SCOP Multidrug efflux transporter AcrB transmembrane domain UniProtKB/TrEMBL
UniProt A0A8P0N585_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:45135 ENTREZGENE