Pcdhac2 Gene Detail

Summary

• Symbol
  Pcdhac2
• Name
  protocadherin alpha subfamily C, 2
• Synonyms
  CNRc2

• Feature Type
  protein coding gene
• IDs
  MGI:1891443
  NCBI Gene: 353237
• Member of
  Pcdha cluster
• Alliance
  gene page
• Transcription Start Sites
  3 TSS

Location &
Maps

• Sequence Map
  Chr18:37276731-37320716 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 18, 19.46 cM
• Mapping Data
  1 experiment

Strain
Comparison

• SNPs within 2kb
  1137 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1891443	protein coding gene	Chr18:37276556-37320716 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0024309	protein coding gene	Chr18:35538408-35583235 (+)
A/J	MGP_AJ_G0024276	protein coding gene	Chr18:34313359-34357515 (+)
AKR/J	MGP_AKRJ_G0024244	protein coding gene	Chr18:35269293-35313391 (+)
BALB/cJ	MGP_BALBcJ_G0024275	protein coding gene	Chr18:34362228-34406362 (+)
C3H/HeJ	MGP_C3HHeJ_G0024042	protein coding gene	Chr18:35314004-35358175 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0024717	protein coding gene	Chr18:36823463-36867648 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022156	protein coding gene	Chr18:34391800-34436126 (+)
CAST/EiJ	MGP_CASTEiJ_G0023517	protein coding gene	Chr18:35312006-35356123 (+)
CBA/J	MGP_CBAJ_G0024011	protein coding gene	Chr18:37901745-37945878 (+)
DBA/2J	MGP_DBA2J_G0024141	protein coding gene	Chr18:33919589-33963728 (+)
FVB/NJ	MGP_FVBNJ_G0024108	protein coding gene	Chr18:33645457-33689539 (+)
LP/J	MGP_LPJ_G0024225	protein coding gene	Chr18:35632299-35676922 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024137	protein coding gene	Chr18:39174773-39218915 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0024766	protein coding gene	Chr18:35136466-35180644 (+)
PWK/PhJ	MGP_PWKPhJ_G0023261	protein coding gene	Chr18:34156387-34203479 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023066	protein coding gene	Chr18:35395325-35441752 (+)
WSB/EiJ	MGP_WSBEiJ_G0023580	protein coding gene	Chr18:35035536-35081773 (+)

Homology

• Human Ortholog
  PCDHAC2, protocadherin alpha subfamily C, 2

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PCDHAC2, protocadherin alpha subfamily C, 2
  
• Synonyms
  PCDH-ALPHA-C2
• Links
  HGNC:8677

  NCBI Gene ID: 56134

  neXtProt AC: NX_Q9Y5I4

  UniProt: Q9Y5I4

  
  
• Chr Location
  5q31.3; chr5:140966470-141012347 (+)  GRCh38

---

• MGI Vertebrate Homology
  Pcdhac2 stringent orthology
  1 human;1 mouse;2 zebrafish
  
• HCOP
  vertebrate homology predictions: PCDHAC2
• Gene Tree
  Pcdhac2
  

Mutations,
Alleles, and
Phenotypes

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

• All Mutations and Alleles
  8
• Endonuclease-mediated
  1
• Targeted
  5
• Transgenic
  2
• Genomic Mutations
  5 involving Pcdhac2
• Incidental Mutations
  CvDC
• Find Mice (IMSR)
  31 strains or lines available

Mice homozygous for a reporter allele are viable and fertile with no apparent gross phenotype.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  3
• GO References
  2

Expression

• Assay Results
  716
• Tissues
  4
• cDNA Data
  2
• Literature Summary
  6

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase pcdhac2

Sequences &
Gene Models

• All Sequences
  26
• RefSeq
  2
• UniProt
  1
• CCDS
  CCDS29168.1

• Ensembl
  ENSMUSG00000102697 (Evidence)
• NCBI Gene
  353237

Representative Sequences			Length	Strain/Species
genomic	353237	NCBI Gene Model | MGI Sequence Detail	43986	C57BL/6J
transcript	NM_001003672	RefSeq | MGI Sequence Detail	5719	C57BL/6
polypeptide	NP_001003672	RefSeq | MGI Sequence Detail	1006	C57BL/6

Protein
Information

• UniProt
  1 Sequence
• PDB
  4ZPM
• InterPro Domains
  IPR020894 Cadherin conserved site
  IPR031904 Cadherin, C-terminal catenin-binding domain
  IPR032455 Cadherin, cytoplasmic C-terminal domain
  IPR002126 Cadherin-like
  IPR015919 Cadherin-like superfamily
  IPR013164 Cadherin, N-terminal
  IPR050174 Protocadherin/Cadherin-related Cell Adhesion
• GlyGen
  Q91Y09 7 sites, 5 N-linked glycans (5 sites)

Molecular
Reagents

• All nucleic 5

  cDNA 2

  Primer pair 3

References

• Summaries
  All 30

  Developmental Gene Expression 6

  Gene Ontology 2

  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 Pcdhac2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr150691	Chr18:37276717-37276749 (+)	2 bp
Tssr150692	Chr18:37276767-37276782 (+)	44 bp
Tssr150693	Chr18:37319748-37319749 (+)	43,018 bp