Pcdha10 (protocadherin alpha 10) - Rat Genome Database

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Gene: Pcdha10 (protocadherin alpha 10) Mus musculus
Analyze
No known orthologs.
Symbol: Pcdha10
Name: protocadherin alpha 10
RGD ID: 1614468
MGI Page MGI
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Located in membrane. Is expressed in brain. Orthologous to human PCDHA12 (protocadherin alpha 12).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cadherin-related neuronal receptor 3; Cn; Cnr3; Cnr8; Cr; Crnr3; Crnr8; PCDH-alpha-10; Pcdha; Pcdha14; protocadherin alpha 14; protocadherin alpha-10; protocadherin alpha-12
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,138,373 - 37,320,710 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1837,138,256 - 37,320,710 (+)EnsemblGRCm39 Ensembl
GRCm381837,005,320 - 37,187,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,005,203 - 37,187,657 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,164,974 - 37,347,311 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361837,131,294 - 37,313,631 (+)NCBIMGSCv36mm8
MGSCv361837,192,426 - 37,374,763 (+)NCBIMGSCv36mm8
Celera1837,452,093 - 37,454,493 (+)NCBICelera
Cytogenetic Map18B3NCBI
cM Map1819.46NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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:12477932   PMID:14672974   PMID:15347688   PMID:15570159   PMID:15640798   PMID:16602821  
PMID:21873635   PMID:24698270   PMID:29911975   PMID:30377227   PMID:32633719  


Genomics

Variants

.
Variants in Pcdha10
6567 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:5838
Count of miRNA genes:542
Interacting mature miRNAs:668
Transcripts:ENSMUST00000007584, ENSMUST00000047479, ENSMUST00000047614, ENSMUST00000070797, ENSMUST00000115657, ENSMUST00000115658, ENSMUST00000115659, ENSMUST00000115661, ENSMUST00000115662
Prediction methods:Miranda, Rnahybrid, Targetscan
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 (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
Pcdha14  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map18B3UniSTS
cM Map18 UniSTS
Pcdha10  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map18B3UniSTS
cM Map18 UniSTS
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


Reference Sequences
RefSeq Acc Id: ENSMUST00000115658   ⟹   ENSMUSP00000111322
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1837,138,256 - 37,320,710 (+)Ensembl
GRCm38.p6 Ensembl1837,005,203 - 37,187,657 (+)Ensembl
RefSeq Acc Id: NM_009961   ⟹   NP_034091
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391837,138,373 - 37,320,710 (+)NCBI
GRCm381837,005,320 - 37,187,657 (+)ENTREZGENE
MGSCv371837,164,974 - 37,347,311 (+)RGD
Celera1837,452,093 - 37,454,493 (+)RGD
cM Map18 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_034091 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK26046 (Get FASTA)   NCBI Sequence Viewer  
  BAA29048 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000111322
  ENSMUSP00000111322.4
GenBank Protein Q91Y20 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_034091   ⟸   NM_009961
- Peptide Label: precursor
- UniProtKB: Q91Y20 (UniProtKB/Swiss-Prot),   O88190 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000111322   ⟸   ENSMUST00000115658
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q91Y20-F1-model_v2 AlphaFold Q91Y20 1-946 view protein structure

Promoters
RGD ID:13677514
Promoter ID:EPDNEW_M22906
Type:initiation region
Name:Pcdha10_1
Description:Mus musculus protocadherin alpha 10 , 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
GRCm381837,005,222 - 37,005,282EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1298408 AgrOrtholog
Ensembl Genes ENSMUSG00000007440 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000115658 ENTREZGENE
  ENSMUST00000115658.6 UniProtKB/Swiss-Prot
Gene3D-CATH Cadherins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:12943 UniProtKB/Swiss-Prot
MGD MGI:1298408 ENTREZGENE
NCBI Gene 12943 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTOCADHERIN ALPHA-9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pcdha10 PhenoGen
PRINTS CADHERIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt O88190 ENTREZGENE, UniProtKB/TrEMBL
  PCDAA_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE