Pcdha6 (protocadherin alpha 6) - Rat Genome Database
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Gene: Pcdha6 (protocadherin alpha 6) Mus musculus
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Symbol: Pcdha6
Name: protocadherin alpha 6
RGD ID: 1614472
MGI Page MGI
Description: Predicted to be involved in cell adhesion. Localizes to membrane. Is expressed in cerebellum and telencephalon. Orthologous to human PCDHA6 (protocadherin alpha 6) and PCDHA8 (protocadherin alpha 8); INTERACTS WITH 1,2-dimethylhydrazine; 4,4'-sulfonyldiphenol; 5-azacytidine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cadherin-related neuronal receptor 2; Cn; CNR; Cnr2; Cr; Crnr2; protocadherin alpha-6
RGD Orthologs
Human
Rat
Dog
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,100,678 - 37,321,950 (+)NCBIGRCm39mm39
GRCm39 Ensembl1837,100,684 - 37,320,710 (+)Ensembl
GRCm381836,967,625 - 37,188,897 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,967,631 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,127,410 - 37,347,311 (+)NCBIGRCm37mm9NCBIm37
MGSCv361837,093,605 - 37,313,631 (+)NCBImm8
Celera1837,414,533 - 37,416,924 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

References

Additional References at PubMed
PMID:9655502   PMID:10380929   PMID:10612399   PMID:10662547   PMID:10716726   PMID:11230163   PMID:11312598   PMID:12477932   PMID:14697259   PMID:15347688   PMID:15570159   PMID:15640798  
PMID:21873635   PMID:23754746   PMID:24698270   PMID:24743017   PMID:29911975   PMID:30377227   PMID:32633719  


Genomics

Comparative Map Data
Pcdha6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,100,678 - 37,321,950 (+)NCBIGRCm39mm39
GRCm39 Ensembl1837,100,684 - 37,320,710 (+)Ensembl
GRCm381836,967,625 - 37,188,897 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,967,631 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,127,410 - 37,347,311 (+)NCBIGRCm37mm9NCBIm37
MGSCv361837,093,605 - 37,313,631 (+)NCBImm8
Celera1837,414,533 - 37,416,924 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
PCDHA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5140,827,958 - 141,012,347 (+)EnsemblGRCh38hg38GRCh38
GRCh385140,827,960 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375140,207,545 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,187,834 - 140,372,113 (+)NCBINCBI36hg18NCBI36
Build 345140,187,833 - 140,372,113NCBI
Celera5136,284,453 - 136,468,708 (+)NCBI
Cytogenetic Map5q31.3NCBI
HuRef5135,352,390 - 135,536,628 (+)NCBIHuRef
CHM1_15139,640,700 - 139,825,092 (+)NCBICHM1_1
Pcdha6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01829,987,206 - 30,215,896 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01829,684,456 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,697,876 - 29,928,030 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11829,724,521 - 29,954,676 (+)NCBI
Celera1828,326,039 - 28,552,754 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHA6
(Canis lupus familiaris - dog)
No map positions available.

Position Markers
Pcdha6  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map18B2-B3UniSTS
cM Map18 UniSTS
PMC311048P3  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381836,998,429 - 36,998,565UniSTSGRCm38
MGSCv371837,158,083 - 37,158,219UniSTSGRCm37
Celera1837,445,202 - 37,445,338UniSTS
Cytogenetic Map18B3UniSTS
Cytogenetic Map18CUniSTS
Cytogenetic Map18B2-B3UniSTS
PMC311048P2  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381837,020,700 - 37,020,817UniSTSGRCm38
MGSCv371837,180,354 - 37,180,471UniSTSGRCm37
Celera1837,467,458 - 37,467,575UniSTS
Cytogenetic Map18CUniSTS
Cytogenetic Map18B3UniSTS
Cytogenetic Map18B2-B3UniSTS
PMC312645P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381837,185,153 - 37,185,340UniSTSGRCm38
MGSCv371837,344,807 - 37,344,994UniSTSGRCm37
Cytogenetic Map18CUniSTS
Cytogenetic Map18B3UniSTS
Cytogenetic Map18B2-B3UniSTS
WI-19540  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381837,187,340 - 37,187,603UniSTSGRCm38
MGSCv371837,346,994 - 37,347,257UniSTSGRCm37
Cytogenetic Map18CUniSTS
Cytogenetic Map18B3UniSTS
Cytogenetic Map18B2-B3UniSTS
RH65516  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381837,186,643 - 37,186,817UniSTSGRCm38
MGSCv371837,346,297 - 37,346,471UniSTSGRCm37
Cytogenetic Map18B2-B3UniSTS
Cytogenetic Map18CUniSTS
Cytogenetic Map18B3UniSTS
PMC311048P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381837,159,265 - 37,159,353UniSTSGRCm38
MGSCv371837,318,919 - 37,319,007UniSTSGRCm37
Cytogenetic Map18CUniSTS
Cytogenetic Map18B3UniSTS
Cytogenetic Map18B2-B3UniSTS
Pcdha  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map18B2-B3UniSTS
Cytogenetic Map18CUniSTS
Cytogenetic Map18B3UniSTS
cM Map18 UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
27226723Tibw9_mtibia width 9, proximal, 16 week (mouse)18320000060800000Mouse
1558849W3q15_mweight 3 weeks QTL 15 (mouse)Not determined18504111961139571Mouse
1558873Hrtfm7_mheart failure modifier 7 (mouse)Not determined18795390741954049Mouse
13504732Cath6_mcarotid atherosclerosis 6 (mouse)181350407347504073Mouse
1357603Mom3_mmodifier of Min 3 (mouse)Not determined181389696666965891Mouse
1300994Pvcan3_mprotection against vaginal candidiasis 3 (mouse)Not determined181606658750066723Mouse
1301307Phospq1_mphospholipid QTL 1 (mouse)Not determined181800665152006806Mouse
1558743Kcal1_mkilocalorie 1 (mouse)Not determined181888582152885939Mouse
1300638Im7_mimmunoregulatory 7 (mouse)Not determined181888582152885939Mouse
11532709Sluc41_msusceptibility to lung cancer 41 (mouse)182082063757457636Mouse
13463476Hctq8_mhematocrit QTL 8 (mouse)182108452755084674Mouse
1301570Sluc14_msusceptibility to lung cancer 14 (mouse)Not determined182248686156487074Mouse
1300877Adip8_madiposity 8 (mouse)Not determined182248686156487074Mouse
11532710Sluc41a_msusceptibility to lung cancer 41a (mouse)182248686156487074Mouse
11532715Sluc41b_msusceptibility to lung cancer 41b (mouse)182248686156487074Mouse
11532716Sluc41c_msusceptibility to lung cancer 41c (mouse)182248686156487074Mouse
4142031Moen1_mmodifier of engrailed QTL 1 (mouse)Not determined182398250757982677Mouse
25823173Hrsq12_mhost response to SARS QTL 12, hemorrhage (mouse)182476282478296340Mouse
12904950Smmq3_msoleus muscle mass QTL 3 (mouse)182592381059923810Mouse
25823167Hrsq5_mhost response to SARS QTL 5, D3% weight (mouse)182710806258694005Mouse
25823171Hrsq10_mhost response to SARS QTL 10, D4% weight (mouse)182710806258694005Mouse
25823174Hrsq11_mhost response to SARS QTL 11, log titer (mouse)182710806258694005Mouse
1301400Lmr13_mleishmaniasis resistance 13 (mouse)Not determined182797631361976451Mouse
4141857Mhysq5_mmale hybrid sterility QTL 5 (mouse)Not determined2799753761997672Mouse
1302163Bmd16_mbone mineral density 16 (mouse)Not determined182953484763534993Mouse
12880412V125Dq12_mvitamin D active form serum level QTL 12 (mouse)183010000064100000Mouse
1300685Scc5_mcolon tumor susceptibility 5 (mouse)Not determined183185541365855562Mouse
1357690Vtbt19_mvertebral trabecular bone trait 19 (mouse)Not determined183295797666958154Mouse
1301771Pcyts6_mplasmacytoma susceptibility 6 (mouse)Not determined183552556069525779Mouse
11041903Lmr27_mleishmaniasis resistance 27 (mouse)183605451444976451Mouse
4142366Chlq10_mcirculating hormone level QTL 10 (mouse)Not determined183615795070158108Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000193389   ⟹   ENSMUSP00000141459
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1836,967,648 - 37,187,388 (+)Ensembl
RefSeq Acc Id: ENSMUST00000193777   ⟹   ENSMUSP00000141587
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1836,967,631 - 37,187,657 (+)Ensembl
RefSeq Acc Id: ENSMUST00000194751   ⟹   ENSMUSP00000142285
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1836,967,650 - 37,187,153 (+)Ensembl
RefSeq Acc Id: NM_007767   ⟹   NP_031793
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391837,100,678 - 37,321,950 (+)NCBI
GRCm381836,967,625 - 37,188,897 (+)NCBI
MGSCv371837,127,410 - 37,347,311 (+)RGD
Celera1837,414,533 - 37,416,914 (+)ENTREZGENE
cM Map18 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_031793 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI50816 (Get FASTA)   NCBI Sequence Viewer  
  AAI50817 (Get FASTA)   NCBI Sequence Viewer  
  AAK26053 (Get FASTA)   NCBI Sequence Viewer  
  BAA29046 (Get FASTA)   NCBI Sequence Viewer  
  BAC84976 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_031793   ⟸   NM_007767
- Peptide Label: precursor
- UniProtKB: Q91Y14 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000141587   ⟸   ENSMUST00000193777
RefSeq Acc Id: ENSMUSP00000141459   ⟸   ENSMUST00000193389
RefSeq Acc Id: ENSMUSP00000142285   ⟸   ENSMUST00000194751
Protein Domains
Cadherin   Cadherin_2

Promoters
RGD ID:13677508
Promoter ID:EPDNEW_M22903
Type:initiation region
Name:Gm38666_1
Description:Mus musculus predicted gene, 38666 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381836,967,556 - 36,967,616EPDNEW
RGD ID:6829466
Promoter ID:MM_KWN:25003
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain
Transcripts:ENSMUST00000063763,   UC008EPA.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361837,129,016 - 37,129,516 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1298367 AgrOrtholog
Ensembl Genes ENSMUSG00000103707 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000141459 UniProtKB/TrEMBL
  ENSMUSP00000141587 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000142285 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000193389 UniProtKB/TrEMBL
  ENSMUST00000193777 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000194751 UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CBD UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
KEGG Report mmu:12937 UniProtKB/TrEMBL
MGD MGI:1298367 ENTREZGENE
NCBI Gene 12937 ENTREZGENE
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdha6 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A0A0A6YY55_MOUSE UniProtKB/TrEMBL
  B9EKB6_MOUSE UniProtKB/TrEMBL
  O88690_MOUSE UniProtKB/TrEMBL
  Q91Y14 ENTREZGENE, UniProtKB/TrEMBL