Pcdhgb8 Pseudogene Detail

Summary

• Symbol
  Pcdhgb8
• Name
  protocadherin gamma subfamily B, 8

• Feature Type
  polymorphic pseudogene
  BioType Conflict
  
• IDs
  MGI:1935200
  NCBI Gene: 93705
• Member of
  Pcdhg cluster
• Alliance
  gene page

Location &
Maps

• Sequence Map
  Chr18:37894854-37973542 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 18, 19.63 cM
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  2156 from dbSNP Build 142
• Strain Annotations
  10

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1935200	polymorphic pseudogene	Chr18:37894854-37974923 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0009940	polymorphic pseudogene	Chr18:36169377-36259974 (+)
A/J	no annotation
AKR/J	no annotation
BALB/cJ	no annotation
C3H/HeJ	no annotation
C57BL/6NJ	MGP_C57BL6NJ_G0010157	polymorphic pseudogene	Chr18:37469332-37559699 (+)
CAROLI/EiJ	no annotation
CAST/EiJ	MGP_CASTEiJ_G0009658	polymorphic pseudogene	Chr18:35892309-35977831 (+)
CBA/J	no annotation
DBA/2J	no annotation
FVB/NJ	MGP_FVBNJ_G0009860	polymorphic pseudogene	Chr18:34239946-34321588 (+)
LP/J	MGP_LPJ_G0009937	polymorphic pseudogene	Chr18:36239546-36321810 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0009826	polymorphic pseudogene	Chr18:39842927-39929362 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0010128	polymorphic pseudogene	Chr18:35741836-35837201 (+)
PWK/PhJ	MGP_PWKPhJ_G0009579	polymorphic pseudogene	Chr18:34734490-34819111 (+)
SPRET/EiJ	no annotation
WSB/EiJ	MGP_WSBEiJ_G0009762	polymorphic pseudogene	Chr18:35646861-35737851 (+)

Homology

• Human Ortholog
  PCDHGB3, protocadherin gamma subfamily B, 3

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PCDHGB3, protocadherin gamma subfamily B, 3
  
• Synonyms
  PCDH-GAMMA-B3
• Links
  HGNC:8710

  NCBI Gene ID: 56102

  neXtProt AC: NX_Q9Y5G1

  UniProt: Q9Y5G1

  
  
• Chr Location
  5q31.3; chr5:141370242-141512975 (+)  GRCh38

---

• Human Ortholog
  PCDHGB8P, protocadherin gamma subfamily B, 8 pseudogene
  
• Synonyms
  PCDH-PSI3
• Links
  HGNC:8715

  NCBI Gene ID: 56120

  
  
• Chr Location
  5q31.3; chr5:141426286-141429158 (+)  GRCh38

---

• MGI Vertebrate Homology
  Pcdhgb8 stringent orthology
  2 human;1 mouse
  
• HCOP
  vertebrate homology predictions: PCDHGB3, PCDHGB8P
• Gene Tree
  Pcdhgb8
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  4 phenotype references
  

• All Mutations and Alleles
  5
• Endonuclease-mediated
  1
• Targeted
  4
• Genomic Mutations
  5 involving Pcdhgb8
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  82 strains or lines available

Gene Ontology
(GO)
Classifications

• All GO Annotations
  1
• GO References
  1

Expression

• Assay Results
  707
• Tissues
  1
• cDNA Data
  2
• Literature Summary
  3

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  23
• RefSeq
  3
• UniProt
  1
• CCDS
  CCDS79634.1

• Ensembl
  ENSMUSG00000103081 (Evidence)
• NCBI Gene
  93705

Representative Sequences			Length	Strain/Species
genomic	93705	NCBI Gene Model | MGI Sequence Detail	78689	C57BL/6J
transcript	NM_033580	RefSeq | MGI Sequence Detail	3234	Not Specified
polypeptide	NP_291058	RefSeq | MGI Sequence Detail	931	Not Specified

Protein
Information

• UniProt
  1 Sequence
• 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

Molecular
Reagents

• All nucleic 6

  Genomic 2

  cDNA 2

  Primer pair 2

References

• Summaries
  All 18

  Developmental Gene Expression 3

  Gene Ontology 1

  Phenotypes 4
• 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