Pcdha1 Gene Detail

Summary

• Symbol
  Pcdha1
• Name
  protocadherin alpha 1

• Feature Type
  protein coding gene
• IDs
  MGI:2150982
  NCBI Gene: 116731
• Member of
  Pcdha cluster
• Alliance
  gene page
• Transcription Start Sites
  1 TSS

Location &
Maps

• Sequence Map
  Chr18:37063338-37320710 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 18, 19.46 cM, cytoband B3
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  7007 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2150982	protein coding gene	Chr18:37063237-37320714 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0024294	protein coding gene	Chr18:35337896-35583239 (+)
A/J	MGP_AJ_G0024260	protein coding gene	Chr18:34106284-34357519 (+)
AKR/J	MGP_AKRJ_G0024228	protein coding gene	Chr18:35077175-35313395 (+)
BALB/cJ	MGP_BALBcJ_G0024260	protein coding gene	Chr18:34149355-34406366 (+)
C3H/HeJ	MGP_C3HHeJ_G0024027	protein coding gene	Chr18:35124668-35358179 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0024701	protein coding gene	Chr18:36588628-36867652 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022141	protein coding gene	Chr18:34201108-34436130 (+)
CAST/EiJ	MGP_CASTEiJ_G0023502	protein coding gene	Chr18:35121109-35356127 (+)
CBA/J	MGP_CBAJ_G0023995	protein coding gene	Chr18:37667465-37945882 (+)
DBA/2J	MGP_DBA2J_G0024127	protein coding gene	Chr18:33721011-33963732 (+)
FVB/NJ	MGP_FVBNJ_G0024094	protein coding gene	Chr18:33433724-33689543 (+)
LP/J	MGP_LPJ_G0024209	protein coding gene	Chr18:35392573-35676926 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024122	protein coding gene	Chr18:38911096-39218919 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0024750	protein coding gene	Chr18:34929727-35180648 (+)
PWK/PhJ	MGP_PWKPhJ_G0023246	protein coding gene	Chr18:33961625-34203483 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023054	protein coding gene	Chr18:35200071-35441756 (+)
WSB/EiJ	MGP_WSBEiJ_G0023565	protein coding gene	Chr18:34837837-35081777 (+)

Homology

• Human Ortholog
  PCDHA1, protocadherin alpha 1

• Vertebrate Orthologs
  11

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PCDHA1, protocadherin alpha 1
  
• Synonyms
  PCDH-ALPHA1
• Links
  HGNC:8663

  NCBI Gene ID: 56147

  neXtProt AC: NX_Q9Y5I3

  UniProt: Q9Y5I3

  
  
• Chr Location
  5q31.3; chr5:140786136-141012347 (+)  GRCh38

---

• MGI Vertebrate Homology
  Pcdha1 stringent orthology
  1 human;1 mouse;10 zebrafish
  
• HCOP
  vertebrate homology predictions: PCDHA1
• Gene Tree
  Pcdha1
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  1 phenotype from 1 allele in 1 genetic background
  8 phenotype references
  

• All Mutations and Alleles
  6
• Endonuclease-mediated
  1
• Targeted
  5
• Genomic Mutations
  5 involving Pcdha1
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  30 strains or lines available

Mice homozygous for a null allele are viable and fertile.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  4
• GO References
  3

Expression

• Assay Results
  728
• Tissues
  8
• cDNA Data
  5
• Literature Summary
  8

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  30
• RefSeq
  2
• UniProt
  2
• CCDS
  CCDS37774.1

• Ensembl
  ENSMUSG00000103442 (Evidence)
• NCBI Gene
  116731

Representative Sequences			Length	Strain/Species
genomic	116731	NCBI Gene Model | MGI Sequence Detail	257373	C57BL/6J
transcript	NM_054072	RefSeq | MGI Sequence Detail	5248	Not Specified
polypeptide	NP_473413	RefSeq | MGI Sequence Detail	948	Not Specified

Protein
Information

• UniProt
  2 Sequences
• InterPro Domains
  IPR020894 Cadherin conserved site
  IPR031904 Cadherin, C-terminal catenin-binding domain
  IPR002126 Cadherin-like
  IPR015919 Cadherin-like superfamily
  IPR013164 Cadherin, N-terminal
  IPR050174 Protocadherin/Cadherin-related Cell Adhesion

Molecular
Reagents

• All nucleic 9

  cDNA 5

  Primer pair 4

  
  

  Microarray probesets 1

References

• Summaries
  All 31

  Developmental Gene Expression 8

  Gene Ontology 3

  Phenotypes 8
• Earliest
  J:67989 Wu Q, et al., Comparative dna sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 2001 Mar;11(3):389-404
• Latest
  J:332241 Kobayashi H, et al., Isoform requirement of clustered protocadherin for preventing neuronal apoptosis and neonatal lethality. iScience. 2023 Jan 20;26(1):105766

TSS for Pcdha1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr150682	Chr18:37069349-37069372 (+)	6,023 bp