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. Located in membrane. Is expressed in brain. Orthologous to several human genes including PCDHA6 (protocadherin alpha 6).
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,100,678 - 37,321,950 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,100,684 - 37,320,710 (+)EnsemblGRCm39 Ensembl
GRCm381836,967,625 - 37,188,897 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,967,631 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,127,410 - 37,347,311 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,093,605 - 37,313,631 (+)NCBIMGSCv36mm8
Celera1837,414,533 - 37,416,924 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
cM Map1819.46NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,100,684 - 37,320,710 (+)EnsemblGRCm39 Ensembl
GRCm381836,967,625 - 37,188,897 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1836,967,631 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,127,410 - 37,347,311 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,093,605 - 37,313,631 (+)NCBIMGSCv36mm8
Celera1837,414,533 - 37,416,924 (+)NCBICelera
Cytogenetic Map18B2- B3NCBI
cM Map1819.46NCBI
PCDHA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,827,960 - 141,012,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,827,958 - 141,012,347 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,207,545 - 140,391,932 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,187,834 - 140,372,113 (+)NCBINCBI36Build 36hg18NCBI36
Build 345140,187,833 - 140,372,113NCBI
Celera5136,284,453 - 136,468,708 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,352,390 - 135,536,628 (+)NCBIHuRef
CHM1_15139,640,843 - 139,825,092 (+)NCBICHM1_1
T2T-CHM13v2.05141,353,294 - 141,537,634 (+)NCBIT2T-CHM13v2.0
Pcdha6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2 Ensembl1828,581,225 - 28,846,211 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01829,987,206 - 30,215,896 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1829,987,206 - 30,215,897 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01829,684,456 - 29,924,443 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41829,697,876 - 29,928,030 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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.

Variants

.
Variants in Pcdha6
8028 total Variants

QTLs in Region (GRCm39)
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)18320000060933072Mouse
1558849W3q15_mweight 3 weeks QTL 15 (mouse)Not determined18504111961272643Mouse
1558873Hrtfm7_mheart failure modifier 7 (mouse)Not determined18808696442087106Mouse
13504732Cath6_mcarotid atherosclerosis 6 (mouse)181363712647637126Mouse
1357603Mom3_mmodifier of Min 3 (mouse)Not determined181403002367098962Mouse
1300994Pvcan3_mprotection against vaginal candidiasis 3 (mouse)Not determined181619964050199776Mouse
1301307Phospq1_mphospholipid QTL 1 (mouse)Not determined181813970452139859Mouse
1300638Im7_mimmunoregulatory 7 (mouse)Not determined181901887453018992Mouse
1558743Kcal1_mkilocalorie 1 (mouse)Not determined181901887453018992Mouse
11532709Sluc41_msusceptibility to lung cancer 41 (mouse)182095369457590708Mouse
13463476Hctq8_mhematocrit QTL 8 (mouse)182121758055217727Mouse
1300877Adip8_madiposity 8 (mouse)Not determined182261991456620127Mouse
11532710Sluc41a_msusceptibility to lung cancer 41a (mouse)182261991456620127Mouse
11532715Sluc41b_msusceptibility to lung cancer 41b (mouse)182261991456620127Mouse
11532716Sluc41c_msusceptibility to lung cancer 41c (mouse)182261991456620127Mouse
1301570Sluc14_msusceptibility to lung cancer 14 (mouse)Not determined182261991456620127Mouse
4142031Moen1_mmodifier of engrailed QTL 1 (mouse)Not determined182411556058115730Mouse
25823173Hrsq12_mhost response to SARS QTL 12, hemorrhage (mouse)182489588178339555Mouse
12904950Smmq3_msoleus muscle mass QTL 3 (mouse)182605687560056875Mouse
25823167Hrsq5_mhost response to SARS QTL 5, D3% weight (mouse)182724111558827077Mouse
25823171Hrsq10_mhost response to SARS QTL 10, D4% weight (mouse)182724111558827077Mouse
25823174Hrsq11_mhost response to SARS QTL 11, log titer (mouse)182724111558827077Mouse
1301400Lmr13_mleishmaniasis resistance 13 (mouse)Not determined182810938062109518Mouse
4141857Mhysq5_mmale hybrid sterility QTL 5 (mouse)Not determined2813060462130739Mouse
1302163Bmd16_mbone mineral density 16 (mouse)Not determined182966791463668060Mouse
12880412V125Dq12_mvitamin D active form serum level QTL 12 (mouse)183023306764233067Mouse
1300685Scc5_mcolon tumor susceptibility 5 (mouse)Not determined183198848065988629Mouse
1357690Vtbt19_mvertebral trabecular bone trait 19 (mouse)Not determined183309104367091221Mouse
1301771Pcyts6_mplasmacytoma susceptibility 6 (mouse)Not determined183565863269658851Mouse
11041903Lmr27_mleishmaniasis resistance 27 (mouse)183618756745109518Mouse
4142366Chlq10_mcirculating hormone level QTL 10 (mouse)Not determined183629102270291180Mouse

Markers in Region
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


Expression


Sequence


RefSeq Acc Id: ENSMUST00000193389   ⟹   ENSMUSP00000141459
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,100,701 - 37,320,441 (+)Ensembl
GRCm38.p6 Ensembl1836,967,648 - 37,187,388 (+)Ensembl
RefSeq Acc Id: ENSMUST00000193777   ⟹   ENSMUSP00000141587
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,100,684 - 37,320,710 (+)Ensembl
GRCm38.p6 Ensembl1836,967,631 - 37,187,657 (+)Ensembl
RefSeq Acc Id: ENSMUST00000194751   ⟹   ENSMUSP00000142285
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,100,703 - 37,320,206 (+)Ensembl
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:
RefSeq Acc Id: NP_031793   ⟸   NM_007767
- Peptide Label: precursor
- UniProtKB: Q91Y14 (UniProtKB/TrEMBL),   O88690 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000141587   ⟸   ENSMUST00000193777
RefSeq Acc Id: ENSMUSP00000141459   ⟸   ENSMUST00000193389
RefSeq Acc Id: ENSMUSP00000142285   ⟸   ENSMUST00000194751
Protein Domains
Cadherin   Cadherin N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q91Y14-F1-model_v2 AlphaFold Q91Y14 1-946 view protein structure

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 Transcript ENSMUST00000193389.2 UniProtKB/TrEMBL
  ENSMUST00000193777 ENTREZGENE
  ENSMUST00000193777.6 UniProtKB/TrEMBL
  ENSMUST00000194751.2 UniProtKB/TrEMBL
Gene3D-CATH Cadherins 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
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-6-RELATED UniProtKB/TrEMBL
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 ENTREZGENE, UniProtKB/TrEMBL
  Q91Y14 ENTREZGENE, UniProtKB/TrEMBL