PCDH1 (protocadherin 1) - Rat Genome Database

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Gene: PCDH1 (protocadherin 1) Chlorocebus sabaeus
Analyze
Symbol: PCDH1
Name: protocadherin 1
RGD ID: 18506215
Description: ENCODES a protein that exhibits calcium ion binding (inferred); INVOLVED IN cell adhesion (inferred); homophilic cell adhesion via plasma membrane adhesion molecules (inferred); ASSOCIATED WITH familial adenomatous polyposis 1 (ortholog); genetic disease (ortholog); Hereditary Neoplastic Syndromes (ortholog); FOUND IN cell junction (inferred); intracellular membrane-bounded organelle (inferred); membrane (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: protocadherin-1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12344,483,355 - 44,510,131 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2344,481,056 - 44,500,780 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603433,341,659 - 33,368,634 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
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

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
PCDH1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12344,483,355 - 44,510,131 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2344,481,056 - 44,500,780 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603433,341,659 - 33,368,634 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
PCDH1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385141,853,090 - 141,878,410 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5141,853,090 - 141,879,246 (-)EnsemblGRCh38hg38GRCh38
GRCh375141,232,655 - 141,257,975 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365141,212,856 - 141,238,128 (-)NCBINCBI36Build 36hg18NCBI36
Build 345141,212,858 - 141,238,128NCBI
Celera5137,309,824 - 137,335,077 (-)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5136,376,728 - 136,401,983 (-)NCBIHuRef
CHM1_15140,666,027 - 140,691,306 (-)NCBICHM1_1
T2T-CHM13v2.05142,379,045 - 142,404,656 (-)NCBIT2T-CHM13v2.0
Pcdh1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391838,318,967 - 38,345,023 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1838,318,967 - 38,345,106 (-)EnsemblGRCm39 Ensembl
GRCm381838,185,914 - 38,212,048 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1838,185,914 - 38,212,053 (-)EnsemblGRCm38mm10GRCm38
MGSCv371838,356,348 - 38,369,416 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361838,322,668 - 38,335,736 (-)NCBIMGSCv36mm8
Celera1839,540,949 - 39,554,018 (-)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1820.08NCBI
Pcdh1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81830,258,154 - 30,290,828 (-)NCBIGRCr8
mRatBN7.21830,011,692 - 30,039,679 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1830,013,185 - 30,039,318 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01831,330,081 - 31,343,147 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1831,328,919 - 31,343,797 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01831,011,244 - 31,023,532 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41831,110,955 - 31,124,786 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11831,137,850 - 31,157,777 (-)NCBI
Celera1829,658,359 - 29,671,795 (-)NCBICelera
Cytogenetic Map18p11NCBI
Pcdh1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541511,916,092 - 11,934,658 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541511,916,095 - 11,934,658 (+)NCBIChiLan1.0ChiLan1.0
PCDH1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24137,097,517 - 137,125,958 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15135,237,073 - 135,265,510 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05137,209,537 - 137,237,977 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15143,323,710 - 143,349,575 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5143,324,641 - 143,345,042 (-)Ensemblpanpan1.1panPan2
PCDH1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1236,813,663 - 36,836,941 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl236,813,657 - 36,836,497 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha233,863,495 - 33,889,885 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0237,265,925 - 37,292,153 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl237,265,589 - 37,291,537 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1234,340,392 - 34,366,791 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0235,151,686 - 35,177,896 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0235,959,180 - 35,985,407 (-)NCBIUU_Cfam_GSD_1.0
Pcdh1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213150,723,092 - 150,746,625 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650412,296,324 - 12,320,611 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493650412,293,889 - 12,320,598 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCDH1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2143,475,935 - 143,501,487 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12143,475,931 - 143,501,204 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22149,679,040 - 149,699,032 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pcdh1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247741,071,155 - 1,097,854 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247741,071,155 - 1,097,960 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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 hemolymphoid system nervous system
High
Medium 15 55
Low 21 19 5
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000010516   ⟹   ENSCSAP00000008608
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl2344,481,056 - 44,500,780 (-)Ensembl
RefSeq Acc Id: XM_008014766   ⟹   XP_008012957
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.12344,483,355 - 44,509,713 (-)NCBI
Vero_WHO_p1.0NW_02366603433,341,996 - 33,368,634 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008014767   ⟹   XP_008012958
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.12344,484,557 - 44,510,131 (-)NCBI
Vero_WHO_p1.0NW_02366603433,341,659 - 33,368,634 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008014769   ⟹   XP_008012960
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.12344,493,955 - 44,502,775 (-)NCBI
Vero_WHO_p1.0NW_02366603433,347,247 - 33,357,840 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038006726   ⟹   XP_037862654
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366603433,341,996 - 33,366,484 (+)NCBI
Protein Sequences
Protein RefSeqs XP_008012957 (Get FASTA)   NCBI Sequence Viewer  
  XP_008012958 (Get FASTA)   NCBI Sequence Viewer  
  XP_008012960 (Get FASTA)   NCBI Sequence Viewer  
  XP_037862654 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000008608
  ENSCSAP00000008608.1
Reference Protein Sequences
RefSeq Acc Id: XP_008012957   ⟸   XM_008014766
- Peptide Label: isoform X1
- UniProtKB: A0A0D9RJ19 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_008012958   ⟸   XM_008014767
- Peptide Label: isoform X2
- UniProtKB: A0A0D9RJ19 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_008012960   ⟸   XM_008014769
- Peptide Label: isoform X4
- UniProtKB: A0A0D9RJ19 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000008608   ⟸   ENSCSAT00000010516
RefSeq Acc Id: XP_037862654   ⟸   XM_038006726
- Peptide Label: isoform X3
- UniProtKB: A0A0D9RJ19 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000012421 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000010516.1 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  Protocadherin UniProtKB/TrEMBL
NCBI Gene PCDH1 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN-1 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Protocadherin UniProtKB/TrEMBL
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/TrEMBL
UniProt A0A0D9RJ19 ENTREZGENE, UniProtKB/TrEMBL