Pcdhga5 Gene Detail

Summary

• Symbol
  Pcdhga5
• Name
  protocadherin gamma subfamily A, 5

• Feature Type
  protein coding gene
• IDs
  MGI:1935217
  NCBI Gene: 93713
• Member of
  Pcdhg cluster
• Alliance
  gene page
• Transcription Start Sites
  2 TSS

Location &
Maps

• Sequence Map
  Chr18:37827433-37974926 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 18, 19.55 cM
• Mapping Data
  3 experiments

Strain
Comparison

• SNPs within 2kb
  1805 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1935217	protein coding gene	Chr18:37827428-37974926 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0024339	protein coding gene	Chr18:36097668-36259977 (+)
A/J	MGP_AJ_G0024307	protein coding gene	Chr18:34862719-35011794 (+)
AKR/J	MGP_AKRJ_G0024275	protein coding gene	Chr18:35819477-35972570 (+)
BALB/cJ	MGP_BALBcJ_G0024306	protein coding gene	Chr18:34928862-35077409 (+)
C3H/HeJ	MGP_C3HHeJ_G0024072	protein coding gene	Chr18:35883069-36038769 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0024748	protein coding gene	Chr18:37394500-37559702 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022187	protein coding gene	Chr18:34877839-35028291 (+)
CAST/EiJ	MGP_CASTEiJ_G0023548	protein coding gene	Chr18:35820134-35977834 (+)
CBA/J	MGP_CBAJ_G0024042	protein coding gene	Chr18:38503459-38667943 (+)
DBA/2J	MGP_DBA2J_G0024172	protein coding gene	Chr18:34463332-34611340 (+)
FVB/NJ	MGP_FVBNJ_G0024138	protein coding gene	Chr18:34172350-34321591 (+)
LP/J	MGP_LPJ_G0024256	protein coding gene	Chr18:36171863-36321813 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024169	protein coding gene	Chr18:39772762-39929365 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0024797	protein coding gene	Chr18:35674706-35837204 (+)
PWK/PhJ	MGP_PWKPhJ_G0023292	protein coding gene	Chr18:34665958-34819114 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023097	protein coding gene	Chr18:35901097-36054330 (+)
WSB/EiJ	MGP_WSBEiJ_G0023610	protein coding gene	Chr18:35573275-35737854 (+)

Homology

• Gene Tree
  Pcdhga5
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  2 phenotype references
  

• All Mutations and Alleles
  3
• Targeted
  3
• Genomic Mutations
  3 involving Pcdhga5
• Incidental Mutations
  CvDC
• Find Mice (IMSR)
  62 strains or lines available

Gene Ontology
(GO)
Classifications

• All GO Annotations
  1
• GO References
  1

Expression

• Assay Results
  672
• cDNA Data
  5
• Literature Summary
  4

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Interactions

• Pcdhga5 interacts with 16 markers (Mir1b, Mir133a-1, Mir133a-2, ...) View All

Sequences &
Gene Models

• All Sequences
  34
• RefSeq
  2
• UniProt
  3
• CCDS
  CCDS79627.1

• Ensembl
  ENSMUSG00000103567 (Evidence)
• NCBI Gene
  93713

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000103567	Ensembl Gene Model | MGI Sequence Detail	147494	C57BL/6J
transcript	ENSMUST00000193414	Ensembl | MGI Sequence Detail	4664	Not Applicable
polypeptide	ENSMUSP00000141893	Ensembl | MGI Sequence Detail	932	Not Applicable

Protein
Information

• UniProt
  3 Sequences
• 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

Molecular
Reagents

• All nucleic 7

  Genomic 2

  cDNA 5

References

• Summaries
  All 21

  Developmental Gene Expression 4

  Gene Ontology 1

  Phenotypes 2
• 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:293992 Mancia Leon WR, et al., Clustered gamma-protocadherins regulate cortical interneuron programmed cell death. Elife. 2020 Jul 7;9

TSS for Pcdhga5:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr150720	Chr18:37827413-37827441 (+)	-6 bp
Tssr150721	Chr18:37827460-37827476 (+)	35 bp