Pcdha6 Gene Detail

Summary

• Symbol
  Pcdha6
• Name
  protocadherin alpha 6
• Synonyms
  Cnr2, Crnr2

• Feature Type
  protein coding gene
• IDs
  MGI:1298367
  NCBI Gene: 12937
• Member of
  Pcdha cluster
• Alliance
  gene page
• Transcription Start Sites
  1 TSS

Location &
Maps

• Sequence Map
  Chr18:37100684-37320710 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

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

Strain
Comparison

• SNPs within 2kb
  5662 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1298367	protein coding gene	Chr18:37100678-37321950 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0024300	protein coding gene	Chr18:35380864-35583235 (+)
A/J	MGP_AJ_G0024266	protein coding gene	Chr18:34143652-34357515 (+)
AKR/J	MGP_AKRJ_G0024234	protein coding gene	Chr18:35114584-35313391 (+)
BALB/cJ	MGP_BALBcJ_G0024266	protein coding gene	Chr18:34191694-34406362 (+)
C3H/HeJ	MGP_C3HHeJ_G0024033	protein coding gene	Chr18:35162068-35358175 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0024707	protein coding gene	Chr18:36629695-36867648 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022147	protein coding gene	Chr18:34238886-34436126 (+)
CAST/EiJ	MGP_CASTEiJ_G0023508	protein coding gene	Chr18:35163321-35356123 (+)
CBA/J	MGP_CBAJ_G0024001	protein coding gene	Chr18:37710533-37945878 (+)
DBA/2J	MGP_DBA2J_G0024133	protein coding gene	Chr18:33758418-33963728 (+)
FVB/NJ	MGP_FVBNJ_G0024099	protein coding gene	Chr18:33472430-33689539 (+)
LP/J	MGP_LPJ_G0024213	protein coding gene	Chr18:35415090-35425472 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024128	protein coding gene	Chr18:38959666-39218915 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0024756	protein coding gene	Chr18:34967904-35180644 (+)
PWK/PhJ	MGP_PWKPhJ_G0023252	protein coding gene	Chr18:34000941-34203479 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023067	protein coding gene	Chr18:35395716-35441752 (+)
WSB/EiJ	MGP_WSBEiJ_G0023571	protein coding gene	Chr18:34878267-35081773 (+)

Homology

• Human Ortholog
  PCDHA6, protocadherin alpha 6

• Vertebrate Orthologs
  11

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PCDHA6, protocadherin alpha 6
  
• Synonyms
  CNR2, CNRN2, CNRS2, CRNR2, PCDH-ALPHA6
• Links
  HGNC:8672

  NCBI Gene ID: 56142

  neXtProt AC: NX_Q9UN73

  UniProt: Q9UN73

  
  
• Chr Location
  5q31.3; chr5:140827958-141012347 (+)  GRCh38

---

• Human Ortholog
  PCDHA8, protocadherin alpha 8
  
• Synonyms
  PCDH-ALPHA8
• Links
  HGNC:8674

  NCBI Gene ID: 56140

  neXtProt AC: NX_Q9Y5H6

  UniProt: Q9Y5H6

  
  
• Chr Location
  5q31.3; chr5:140841187-141012347 (+)  GRCh38

---

• MGI Vertebrate Homology
  Pcdha6 stringent orthology
  2 human;1 mouse;9 zebrafish
  
• HCOP
  vertebrate homology predictions: PCDHA6, PCDHA8
• Gene Tree
  Pcdha6
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  6 phenotype references
  

• All Mutations and Alleles
  5
• Endonuclease-mediated
  1
• Targeted
  4
• Genomic Mutations
  5 involving Pcdha6
• Find Mice (IMSR)
  29 strains or lines available

Gene Ontology
(GO)
Classifications

• All GO Annotations
  3
• GO References
  2

Expression

• Assay Results
  727
• Tissues
  15
• cDNA Data
  3
• Literature Summary
  8

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  37
• RefSeq
  2
• UniProt
  4
• CCDS
  CCDS79618.1

• Ensembl
  ENSMUSG00000103707 (Evidence)
• NCBI Gene
  12937

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000103707	Ensembl Gene Model | MGI Sequence Detail	220027	C57BL/6J
transcript	ENSMUST00000193777	Ensembl | MGI Sequence Detail	5367	Not Applicable
polypeptide	ENSMUSP00000141587	Ensembl | MGI Sequence Detail	946	Not Applicable

Protein
Information

• UniProt
  4 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
• GlyGen
  Q91Y14 2 sites, 2 N-linked glycans (2 sites)

Molecular
Reagents

• All nucleic 10

  Genomic 2

  cDNA 3

  Primer pair 4

  Other 1

  
  

  Microarray probesets 1

References

• Summaries
  All 28

  Developmental Gene Expression 8

  Gene Ontology 2

  Phenotypes 6
• Earliest
  J:48282 Kohmura N, et al., Diversity revealed by a novel family of cadherins expressed in neurons at a synaptic complex. Neuron. 1998 Jun;20(6):1137-51
• 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 Pcdha6:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr150688	Chr18:37100672-37100703 (+)	4 bp