Pcdh9 Gene Detail

Summary

• Symbol
  Pcdh9
• Name
  protocadherin 9
• Synonyms
  1500001L12Rik, A730003J17Rik, C530050I23Rik, C630029H24Rik, LOC382930

• Feature Type
  protein coding gene
• IDs
  MGI:1306801
  NCBI Gene: 211712
• Alliance
  gene page
• Transcription Start Sites
  27 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr14:93250846-94128115 bp, - strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 14, 45.80 cM
• Mapping Data
  5 experiments

Strain
Comparison

• SNPs within 2kb
  26013 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1306801	protein coding gene	Chr14:93250846-94132619 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0021610	protein coding gene	Chr14:88874903-89814765 (-)
A/J	MGP_AJ_G0021568	protein coding gene	Chr14:86304495-87162946 (-)
AKR/J	MGP_AKRJ_G0021544	protein coding gene	Chr14:88857081-89742657 (-)
BALB/cJ	MGP_BALBcJ_G0021574	protein coding gene	Chr14:86441814-87322365 (-)
C3H/HeJ	MGP_C3HHeJ_G0021352	protein coding gene	Chr14:88642437-89546593 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0022014	protein coding gene	Chr14:92569227-93533240 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0019554	protein coding gene	Chr14:83572750-84417095 (-)
CAST/EiJ	MGP_CASTEiJ_G0020869	protein coding gene	Chr14:85757361-86690274 (-)
CBA/J	MGP_CBAJ_G0021320	protein coding gene	Chr14:95790788-96805134 (-)
DBA/2J	MGP_DBA2J_G0021444	protein coding gene	Chr14:85712955-86599263 (-)
FVB/NJ	MGP_FVBNJ_G0021420	protein coding gene	Chr14:84812718-85682919 (-)
LP/J	MGP_LPJ_G0021512	protein coding gene	Chr14:89756767-90699919 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0021448	protein coding gene	Chr14:97172865-98456400 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022037	protein coding gene	Chr14:88252475-89167594 (-)
PWK/PhJ	MGP_PWKPhJ_G0020612	protein coding gene	Chr14:82568617-83466678 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0020450	protein coding gene	Chr14:84161957-85064127 (-)
WSB/EiJ	MGP_WSBEiJ_G0020922	protein coding gene	Chr14:88773480-89693792 (-)

Homology

• Human Ortholog
  PCDH9, protocadherin 9

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PCDH9, protocadherin 9
  
• Links
  HGNC:8661

  NCBI Gene ID: 5101

  neXtProt AC: NX_Q9HC56

  UniProt: Q9HC56

  
  
• Chr Location
  13q21.32; chr13:66302834-67230445 (-)  GRCh38

---

• MGI Vertebrate Homology
  Pcdh9 stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: PCDH9
• Gene Tree
  Pcdh9
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  19 phenotypes from 2 alleles in 2 genetic backgrounds
  9 phenotype references
  

• All Mutations and Alleles
  5
• Chemically induced (other)
  1
• Endonuclease-mediated
  1
• Targeted
  3
• Genomic Mutations
  1 involving Pcdh9
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  65 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit impaired long-term social and bject recognition and sensorimotor development.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  6
• GO References
  4

Expression

• Assay Results
  914
• Tissues
  167
• cDNA Data
  23
• Literature Summary
  17

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GENSAT
  GEO
  Expression Atlas
• Other Vertebrate Links
  GEISHA PCDH9
  Xenbase pcdh9

Sequences &
Gene Models

• All Sequences
  89
• RefSeq
  17
• UniProt
  15
• CCDS
  CCDS36992.1, CCDS79350.1, CCDS79352.1, CCDS84156.1

• Ensembl
  ENSMUSG00000055421 (Evidence)
• NCBI Gene
  211712

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000055421	Ensembl Gene Model | MGI Sequence Detail	877270	C57BL/6J
transcript	ENSMUST00000068992	Ensembl | MGI Sequence Detail	3714	Not Applicable
polypeptide	ENSMUSP00000070935	Ensembl | MGI Sequence Detail	1237	Not Applicable

Protein
Information

• UniProt
  15 Sequences
• InterPro Domains
  IPR020894 Cadherin conserved site
  IPR002126 Cadherin-like
  IPR015919 Cadherin-like superfamily
  IPR013164 Cadherin, N-terminal
  IPR013585 Protocadherin
  IPR050174 Protocadherin/Cadherin-related Cell Adhesion
• GlyGen
  F8VPK8 13 sites, 24 N-linked glycans (13 sites)

Molecular
Reagents

• All nucleic 32

  cDNA 26

  Primer pair 3

  Other 3

  
  

  Microarray probesets 9

Other
Accession IDs

MGI:1916209, MGI:2444471, MGI:2685143, MGI:2686059, MGI:3510991

References

• Summaries
  All 44

  Developmental Gene Expression 17

  Gene Ontology 4

  Phenotypes 9
• Earliest
  J:50455 Strehl S, et al., Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14. Genomics. 1998 Oct 1;53(1):81-9
• Latest
  J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Pcdh9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr129977	Chr14:94128128-94128152 (-)	-25 bp
Tssr129976	Chr14:94128110-94128125 (-)	-3 bp
Tssr129975	Chr14:94114740-94114759 (-)	13,365 bp
Tssr129974	Chr14:94114411-94114417 (-)	13,701 bp
Tssr129973	Chr14:94110873-94110882 (-)	17,237 bp
Tssr129972	Chr14:94104676-94104687 (-)	23,433 bp
Tssr129971	Chr14:94104634-94104664 (-)	23,466 bp
Tssr129970	Chr14:94079091-94079109 (-)	49,015 bp
Tssr129969	Chr14:94078508-94078513 (-)	49,604 bp
Tssr129968	Chr14:94049804-94049818 (-)	78,304 bp
Tssr129967	Chr14:94049714-94049748 (-)	78,384 bp
Tssr129966	Chr14:94047248-94047271 (-)	80,855 bp
Tssr129964	Chr14:94003494-94003502 (-)	124,617 bp
Tssr129963	Chr14:93956668-93956685 (-)	171,438 bp
Tssr129962	Chr14:93955472-93955486 (-)	172,636 bp
Tssr129961	Chr14:93948196-93948200 (-)	179,917 bp
Tssr129960	Chr14:93938345-93938350 (-)	189,767 bp
Tssr129959	Chr14:93938253-93938271 (-)	189,853 bp
Tssr129958	Chr14:93922708-93922719 (-)	205,401 bp
Tssr129957	Chr14:93922623-93922634 (-)	205,486 bp
Tssr129956	Chr14:93875791-93875809 (-)	252,315 bp
Tssr129953	Chr14:93735522-93735527 (-)	392,590 bp
Tssr129952	Chr14:93709460-93709473 (-)	418,648 bp
Tssr129951	Chr14:93609184-93609188 (-)	518,929 bp
Tssr129950	Chr14:93494347-93494352 (-)	633,765 bp
Tssr129949	Chr14:93462353-93462356 (-)	665,760 bp
Tssr129944	Chr14:93317151-93317161 (-)	810,959 bp

Pcdh9 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Ccmsa2	Chr14, syntenic		J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).

*cM position of peak correlated region/marker