Prkca Gene Detail

Summary

• Symbol
  Prkca
• Name
  protein kinase C, alpha
• Synonyms
  Pkca

• Feature Type
  protein coding gene
• IDs
  MGI:97595
  NCBI Gene: 18750
• Alliance
  gene page
• Transcription Start Sites
  21 TSS
• Candidate for QTL
  3 QTL

Location &
Maps

• Sequence Map
  Chr11:107824213-108234754 bp, - strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 11, 70.80 cM
• Mapping Data
  37 experiments

Strain
Comparison

• SNPs within 2kb
  2685 from dbSNP Build 142
• Strain Annotations
  18
• RFLP
  5

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_97595	protein coding gene	Chr11:107824213-108237360 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0019325	protein coding gene	Chr11:111371037-111810071 (-)
A/J	MGP_AJ_G0019293	protein coding gene	Chr11:106589537-106998980 (-)
AKR/J	MGP_AKRJ_G0019262	protein coding gene	Chr11:109780094-110199485 (-)
BALB/cJ	MGP_BALBcJ_G0019267	protein coding gene	Chr11:107015121-107429715 (-)
C3H/HeJ	MGP_C3HHeJ_G0019076	protein coding gene	Chr11:110088780-110515861 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0019717	protein coding gene	Chr11:114792752-115216661 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017341	protein coding gene	Chr11:103853385-104264497 (-)
CAST/EiJ	MGP_CASTEiJ_G0018629	protein coding gene	Chr11:111195888-111625093 (-)
CBA/J	MGP_CBAJ_G0019045	protein coding gene	Chr11:119540387-120000489 (-)
DBA/2J	MGP_DBA2J_G0019157	protein coding gene	Chr11:106070209-106477226 (-)
FVB/NJ	MGP_FVBNJ_G0019148	protein coding gene	Chr11:105577187-105984327 (-)
LP/J	MGP_LPJ_G0019227	protein coding gene	Chr11:111811054-112241563 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019178	protein coding gene	Chr11:118745379-119180835 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0019754	protein coding gene	Chr11:110336438-110765390 (-)
PWK/PhJ	MGP_PWKPhJ_G0018394	protein coding gene	Chr11:107217822-107635355 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0018185	protein coding gene	Chr11:110091118-110511473 (-)
WSB/EiJ	MGP_WSBEiJ_G0018680	protein coding gene	Chr11:110276224-110698202 (-)

Homology

• Human Ortholog
  PRKCA, protein kinase C alpha

• Vertebrate Orthologs
  4

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  PRKCA, protein kinase C alpha
  
• Synonyms
  AAG6, PKCA, PKCalpha, PKC-alpha, PKCI+/-, PRKACA
• Links
  HGNC:9393

  NCBI Gene ID: 5578

  neXtProt AC: NX_P17252

  UniProt: P17252

  
  
• Chr Location
  17q24.2; chr17:66302613-66810743 (+)  GRCh38

---

• Alliance of Genome Resources
  Prkca stringent orthology
  1 human;1 mouse;1 rat;2 zebrafish
  
• HCOP
  vertebrate homology predictions: PRKCA
• Protein SuperFamily
  PKC_alpha
• Gene Tree
  Prkca
  

Human Diseases

• Diseases
  6 with human PRKCA associations

				Human Disease	Mouse Models
				chordoid glioma IDs chordoid glioma       DOID:3774 NCI:C5592 ORDO:251674 UMLS_CUI:C1322252
				dilated cardiomyopathy IDs dilated cardiomyopathy       DOID:12930 EFO:0000407 ICD10CM:I42.0 KEGG:05414 MESH:D002311 NCI:C84673 OMIM:PS115200 ORDO:217604 UMLS_CUI:C0007193
				high grade glioma IDs high grade glioma       DOID:3070 DOID:2627 KEGG:05214 MESH:D005910 NCI:C3059 NCI:C4822 OMIM:PS137800 ORDO:182067 UMLS_CUI:C0017638 UMLS_CUI:C0555198
				large cell carcinoma IDs large cell carcinoma       DOID:4552 MESH:D018287 NCI:C3780 UMLS_CUI:C0206704
				ovarian cancer IDs ovarian cancer       DOID:2394 DOID:0060070 DOID:2144 DOID:9595 ICD10CM:C56 ICD9CM:183.0 MESH:D010051 NCI:C4984 NCI:C7431 OMIM:167000 OMIM:607893 ORDO:213500 ORDO:213517 UMLS_CUI:C0919267 UMLS_CUI:C1140680 UMLS_CUI:C1299247
				prostate carcinoma IDs prostate carcinoma       DOID:10286 EFO:0001663 KEGG:05215 NCI:C4863 UMLS_CUI:C0600139

Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  11 phenotypes from 3 alleles in 4 genetic backgrounds
  4 phenotypes from multigenic genotypes
  82 phenotype references
  

• All Mutations and Alleles
  15
• Endonuclease-mediated
  4
• Gene trapped
  5
• Targeted
  3
• Transgenic
  3
• Incidental Mutations
  Mutagenetix , APF , CvDC
• Find Mice (IMSR)
  33 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Homozygous null mice show no overt macroscopic abnormalities, however examination of one line revealed increased cardiac muscle contractility and protection against heart failure.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  121
• GO References
  39

Expression

• Assay Results
  1048
• Tissues
  194
• cDNA Data
  72
• Literature Summary
  145

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase prkca
  ZFIN prkcaa, prkcab

Interactions

• Prkca interacts with 478 markers (Mir7-1, Mir7-2, Mir7b, ...) View All

Sequences &
Gene Models

• All Sequences
  45
• RefSeq
  4
• UniProt
  3
• CCDS
  CCDS25573.1

• Ensembl
  ENSMUSG00000050965 (Evidence)
• NCBI Gene
  18750

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000050965	Ensembl Gene Model | MGI Sequence Detail	410542	C57BL/6J
transcript	ENSMUST00000059595	Ensembl | MGI Sequence Detail	8409	Not Applicable
polypeptide	ENSMUSP00000062392	Ensembl | MGI Sequence Detail	672	Not Applicable

Protein
Information

• UniProt
  3 Sequences
• Protein Ontology
  PR:000003058 protein kinase C alpha type
  (term hierarchy)
• PDB
  6UWA
• EC
  2.7.11.13
• InterPro Domains
  IPR000961 AGC-kinase, C-terminal
  IPR046349 C1-like domain superfamily
  IPR000008 C2 domain
  IPR035892 C2 domain superfamily
  IPR034663 Classical Protein Kinase C alpha, catalytic domain
  IPR020454 Diacylglycerol/phorbol-ester binding
  IPR017441 Protein kinase, ATP binding site
  IPR014375 Protein kinase C, alpha/beta/gamma types
  IPR002219 Protein kinase C-like, phorbol ester/diacylglycerol-binding domain
  IPR017892 Protein kinase, C-terminal
  IPR000719 Protein kinase domain
  IPR011009 Protein kinase-like domain superfamily
  IPR008271 Serine/threonine-protein kinase, active site

Molecular
Reagents

• All nucleic 85

  cDNA 74

  Primer pair 9

  Other 2

  
  

  Microarray probesets 5

Other
Accession IDs

MGD-MRK-13327, MGI:2144325

References

• Summaries
  All 410

  Developmental Gene Expression 145

  Gene Ontology 39

  Phenotypes 82
• Earliest
  J:9748 Rose-John S, et al., Molecular cloning of mouse protein kinase C (PKC) cDNA from Swiss 3T3 fibroblasts. Gene. 1988 Dec 30;74(2):465-71
• Latest
  J:337476 Gredler ML, et al., Multicellular rosettes link mesenchymal-epithelial transition to radial intercalation in the mouse axial mesoderm. Dev Cell. 2023 Jun 5;58(11):933-950.e5

TSS for Prkca:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr111511	Chr11:108234945-108235006 (-)	-222 bp
Tssr111510	Chr11:108234916-108234930 (-)	-169 bp
Tssr111509	Chr11:108234770-108234780 (-)	-21 bp
Tssr111508	Chr11:108234743-108234767 (-)	-1 bp
Tssr111507	Chr11:108234705-108234723 (-)	40 bp
Tssr111506	Chr11:108234681-108234692 (-)	67 bp
Tssr111505	Chr11:108234375-108234394 (-)	369 bp
Tssr111504	Chr11:108212410-108212414 (-)	22,342 bp
Tssr111503	Chr11:108186626-108186629 (-)	48,126 bp
Tssr111502	Chr11:108180994-108180998 (-)	53,758 bp
Tssr111501	Chr11:108164610-108164615 (-)	70,141 bp
Tssr111500	Chr11:108164511-108164553 (-)	70,222 bp
Tssr111499	Chr11:108163132-108163136 (-)	71,620 bp
Tssr111498	Chr11:108161341-108161413 (-)	73,377 bp
Tssr111497	Chr11:108153667-108153678 (-)	81,081 bp
Tssr111496	Chr11:108153510-108153529 (-)	81,234 bp
Tssr111495	Chr11:108152070-108152078 (-)	82,680 bp
Tssr111494	Chr11:108139873-108139876 (-)	94,879 bp
Tssr111493	Chr11:108131854-108131874 (-)	102,890 bp
Tssr111492	Chr11:108117832-108117837 (-)	116,919 bp
Tssr111491	Chr11:107935504-107935509 (-)	299,247 bp

Prkca is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Afw5	Chr11, syntenic		J:123128	A search for candidate genes was performed using DU6 and DU6i high body weight selection lines and lean unselected lines DUKs and DBA/2. RNA from epididymal fat tissue of 20 males from each line (DU6, DU6i, DUKs and DBA2/J) was pooled for analysis in Affymetrix GeneChips and resulted in the identification of 77 differentially expressed candidate genes. Of these, 14 genes are located in QTLs intervals affecting body weight and abdominal fat weight. On mouse Chromosome 4, candidate gene Ak2 (61 cM) is upregulated in selected lines while candidate gene Ubxd5 at 65.7 cM (formerly 4930506L07Rik) is downregulated in selected lines. These genes map to the Afw14 QTL interval at 66 cM. On mouse Chromosome 5, candidate gene Mcm7 is downregulated in selected lines compared to unselected lines. This gene is located near the Afw15 (80 cM) and Bw13 (81 cM) QTL intervals. On mouse Chromosome 7, candidate genes Ldhc (23.5 cM) and Stard10 exhibit decreased expression in selected versus unselected lines. These genes are located near the Afw9 (23 cM) QTL interval. On mouse Chromosome 11, candidate gene Prkca (68 cM) is upregulated in selected lines versus unselected lines. Candidate genes Ero1lb (formerly 1300013B24Rik-*note the current location of this gene according to assembly data inthe Mouse Genome Database is chromosome 13) and EST AA178476 map to the Bw4 QTL interval at 55 cM and display increased expression in selected lines compared to unselected lines. Zpbp is down-regulated in selected lines compared tounselected lines and maps to the Afw5 (10 cM) and Bw16 (14 cM) QTL intervals. On mouse Chromosome 12, candidate gene Serpina3c maps near the Afw10 (21 cM) and Bw9 (17 cM) QTL intervals and is upregulated in selected lines. These genes are upregulated inselected lines compared to unselected lines. Candidate gene Cox8a (*note- the current location of this gene according to data in the Mouse Genome Database is chromosome 19) also maps to the same QTL intervals but is downregulated in selected lines comparedto unselected lines. Candidate gene Igh-1a (58 cM) maps near QTL Afw10 and is upregulated in selected lines compared to unselected lines. On mouse Chromosome 13, candidate genes Hfe (15 cM) and Hist1h1c (formerly H1f2) map near the Afw18 QTL interval (11cM). These genes are upregulated in selected lines compared to unselected lines.
Bw4	Chr11, 50.86 cM		J:123128	A search for candidate genes was performed using DU6 and DU6i high body weight selection lines and lean unselected lines DUKs and DBA/2. RNA from epididymal fat tissue of 20 males from each line (DU6, DU6i, DUKs and DBA2/J) was pooled for analysis in Affymetrix GeneChips and resulted in the identification of 77 differentially expressed candidate genes. Of these, 14 genes are located in QTLs intervals affecting body weight and abdominal fat weight. On mouse Chromosome 4, candidate gene Ak2 (61 cM) is upregulated in selected lines while candidate gene Ubxd5 at 65.7 cM (formerly 4930506L07Rik) is downregulated in selected lines. These genes map to the Afw14 QTL interval at 66 cM. On mouse Chromosome 5, candidate gene Mcm7 is downregulated in selected lines compared to unselected lines. This gene is located near the Afw15 (80 cM) and Bw13 (81 cM) QTL intervals. On mouse Chromosome 7, candidate genes Ldhc (23.5 cM) and Stard10 exhibit decreased expression in selected versus unselected lines. These genes are located near the Afw9 (23 cM) QTL interval. On mouse Chromosome 11, candidate gene Prkca (68 cM) is upregulated in selected lines versus unselected lines. Candidate genes Ero1lb (formerly 1300013B24Rik-*note the current location of this gene according to assembly data inthe Mouse Genome Database is chromosome 13) and EST AA178476 map to the Bw4 QTL interval at 55 cM and display increased expression in selected lines compared to unselected lines. Zpbp is down-regulated in selected lines compared tounselected lines and maps to the Afw5 (10 cM) and Bw16 (14 cM) QTL intervals. On mouse Chromosome 12, candidate gene Serpina3c maps near the Afw10 (21 cM) and Bw9 (17 cM) QTL intervals and is upregulated in selected lines. These genes are upregulated inselected lines compared to unselected lines. Candidate gene Cox8a (*note- the current location of this gene according to data in the Mouse Genome Database is chromosome 19) also maps to the same QTL intervals but is downregulated in selected lines comparedto unselected lines. Candidate gene Igh-1a (58 cM) maps near QTL Afw10 and is upregulated in selected lines compared to unselected lines. On mouse Chromosome 13, candidate genes Hfe (15 cM) and Hist1h1c (formerly H1f2) map near the Afw18 QTL interval (11cM). These genes are upregulated in selected lines compared to unselected lines.
Bw16	Chr11, syntenic		J:123128	A search for candidate genes was performed using DU6 and DU6i high body weight selection lines and lean unselected lines DUKs and DBA/2. RNA from epididymal fat tissue of 20 males from each line (DU6, DU6i, DUKs and DBA2/J) was pooled for analysis in Affymetrix GeneChips and resulted in the identification of 77 differentially expressed candidate genes. Of these, 14 genes are located in QTLs intervals affecting body weight and abdominal fat weight. On mouse Chromosome 4, candidate gene Ak2 (61 cM) is upregulated in selected lines while candidate gene Ubxd5 at 65.7 cM (formerly 4930506L07Rik) is downregulated in selected lines. These genes map to the Afw14 QTL interval at 66 cM. On mouse Chromosome 5, candidate gene Mcm7 is downregulated in selected lines compared to unselected lines. This gene is located near the Afw15 (80 cM) and Bw13 (81 cM) QTL intervals. On mouse Chromosome 7, candidate genes Ldhc (23.5 cM) and Stard10 exhibit decreased expression in selected versus unselected lines. These genes are located near the Afw9 (23 cM) QTL interval. On mouse Chromosome 11, candidate gene Prkca (68 cM) is upregulated in selected lines versus unselected lines. Candidate genes Ero1lb (formerly 1300013B24Rik-*note the current location of this gene according to assembly data inthe Mouse Genome Database is chromosome 13) and EST AA178476 map to the Bw4 QTL interval at 55 cM and display increased expression in selected lines compared to unselected lines. Zpbp is down-regulated in selected lines compared tounselected lines and maps to the Afw5 (10 cM) and Bw16 (14 cM) QTL intervals. On mouse Chromosome 12, candidate gene Serpina3c maps near the Afw10 (21 cM) and Bw9 (17 cM) QTL intervals and is upregulated in selected lines. These genes are upregulated inselected lines compared to unselected lines. Candidate gene Cox8a (*note- the current location of this gene according to data in the Mouse Genome Database is chromosome 19) also maps to the same QTL intervals but is downregulated in selected lines comparedto unselected lines. Candidate gene Igh-1a (58 cM) maps near QTL Afw10 and is upregulated in selected lines compared to unselected lines. On mouse Chromosome 13, candidate genes Hfe (15 cM) and Hist1h1c (formerly H1f2) map near the Afw18 QTL interval (11cM). These genes are upregulated in selected lines compared to unselected lines.

*cM position of peak correlated region/marker