Pdgfra MGI Mouse Gene Detail - MGI:97530 - platelet derived growth factor receptor, alpha polypeptide

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Pdgfra Gene Detail

Symbol

Pdgfra
Name

platelet derived growth factor receptor, alpha polypeptide
Synonyms

CD140a, Pdgfr-2

Feature Type

protein coding gene
IDs

MGI:97530
NCBI Gene: 18595
Alliance

gene page
Transcription Start Sites

15 TSS
Candidate for QTL

5 QTL

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Sequence Map

Chr5:75312953-75358876 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 5, 39.55 cM
Mapping Data

35 experiments

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SNPs within 2kb

1275 from dbSNP Build 142
Strain Annotations

18
RFLP

10

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_97530	protein coding gene	Chr5:75311988-75358876 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0029637	protein coding gene	Chr5:75272496-75321528 (+)
A/J	MGP_AJ_G0029605	protein coding gene	Chr5:72417985-72463684 (+)
AKR/J	MGP_AKRJ_G0029553	protein coding gene	Chr5:74773377-74819490 (+)
BALB/cJ	MGP_BALBcJ_G0029614	protein coding gene	Chr5:73119517-73167632 (+)
C3H/HeJ	MGP_C3HHeJ_G0029337	protein coding gene	Chr5:75158918-75205393 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0030068	protein coding gene	Chr5:78303537-78349133 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0027309	protein coding gene	Chr5:68087175-68132222 (+)
CAST/EiJ	MGP_CASTEiJ_G0028745	protein coding gene	Chr5:74273468-74324456 (+)
CBA/J	MGP_CBAJ_G0029306	protein coding gene	Chr5:80899053-80944561 (+)
DBA/2J	MGP_DBA2J_G0029451	protein coding gene	Chr5:72487557-72534558 (+)
FVB/NJ	MGP_FVBNJ_G0029412	protein coding gene	Chr5:71641990-71691916 (+)
LP/J	MGP_LPJ_G0029538	protein coding gene	Chr5:75704640-75754183 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0029440	protein coding gene	Chr5:84104679-84153109 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0030101	protein coding gene	Chr5:74306542-74359382 (+)
PWK/PhJ	MGP_PWKPhJ_G0028468	protein coding gene	Chr5:71481898-71531947 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0028303	protein coding gene	Chr5:73654603-73717107 (+)
WSB/EiJ	MGP_WSBEiJ_G0028825	protein coding gene	Chr5:74596075-74649079 (+)

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Human Ortholog

PDGFRA, platelet derived growth factor receptor alpha

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PDGFRA, platelet derived growth factor receptor alpha
Synonyms

CD140A, PDGFR-2, PDGFR2
Links

HGNC:8803

NCBI Gene ID: 5156

neXtProt AC: NX_P16234

UniProt: P16234
Chr Location

4q12; chr4:54229280-54298245 (+) GRCh38

MGI Vertebrate Homology

Pdgfra stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: PDGFRA
Protein SuperFamily

TyrPK_CSF1-R
Gene Tree

Pdgfra

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Diseases

2 with Pdgfra mouse models; 6 with human PDGFRA associations

Human Disease

Mouse Models

Mouse gene associated with disease

congenital diaphragmatic hernia

IDs

View 1 model

scimitar syndrome

IDs

View 1 model

Human gene associated with disease

hypereosinophilic syndrome

IDs

IDs

myeloid leukemia

IDs

myeloid sarcoma

IDs

pancreatic cancer

IDs

T-cell acute lymphoblastic leukemia

IDs

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

Mutations/Alleles

1 with disease annotations

References

3 with disease annotations

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Phenotype Summary

135 phenotypes from 12 alleles in 12 genetic backgrounds
81 phenotypes from multigenic genotypes
748 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

49
Chemically induced (other)

2
Endonuclease-mediated

10
Gene trapped

1
Radiation induced

2
Spontaneous

5
Targeted

29
Genomic Mutations

9 involving Pdgfra
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

87 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Homozygotes for targeted null mutations exhibit incomplete cephalic closure, increased apoptosis of neural crest cells, impaired myotome and testis formation, abnormal mucosal linings, thoracic skeletal defects, and midgestational lethality.

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All GO Annotations

145
GO References

34

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

2304
Tissues

756
cDNA Data

48
Literature Summary

552

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA PDGFRA

Xenbase pdgfra

ZFIN pdgfra

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All Sequences

93
RefSeq

15
UniProt

10
CCDS

CCDS19351.1, CCDS89929.1

Ensembl

ENSMUSG00000029231 (Evidence)
NCBI Gene

18595

Representative Sequences				Length	Strain/Species	Flank
	genomic	ENSMUSG00000029231	Ensembl Gene Model \| MGI Sequence Detail	45924	C57BL/6J	± kb
	transcript	ENSMUST00000000476	Ensembl \| MGI Sequence Detail	6549	Not Applicable
	polypeptide	ENSMUSP00000000476	Ensembl \| MGI Sequence Detail	1089	Not Applicable

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UniProt

10 Sequences
Protein Ontology

PR:000002030 alpha-type platelet-derived growth factor receptor

(term hierarchy)
EC

2.7.10.1
InterPro Domains

IPR013098 Immunoglobulin I-set

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR003599 Immunoglobulin subtype

IPR003598 Immunoglobulin subtype 2

IPR027290 Platelet-derived growth factor receptor alpha

IPR042495 Platelet-derived growth factor receptor-like protein

IPR017441 Protein kinase, ATP binding site

IPR000719 Protein kinase domain

IPR011009 Protein kinase-like domain superfamily

IPR050122 Receptor Tyrosine Kinase

IPR001245 Serine-threonine/tyrosine-protein kinase, catalytic domain

IPR008266 Tyrosine-protein kinase, active site

IPR020635 Tyrosine-protein kinase, catalytic domain

IPR001824 Tyrosine-protein kinase, receptor class III, conserved site
GlyGen

P26618 10 sites, 4 N-linked glycans (4 sites)

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All nucleic 126

Genomic 9

cDNA 65

Primer pair 23

Other 29

Microarray probesets 6

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MGD-MRK-13215, MGD-MRK-13216, MGI:2140805

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Summaries

All 1333

Developmental Gene Expression 552

Diseases 3

Gene Ontology 34

Phenotypes 748
Earliest

J:99 Gruneberg H, et al., Two closely linked genes in the mouse. Genet Res. 1960;1(1):69-90
Latest

J:358639 Su Y, et al., Brainstem Dbh(+) neurons control allergen-induced airway hyperreactivity. Nature. 2024 Jul;631(8021):601-609

TSS for Pdgfra:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr46684	Chr5:75312041-75312061 (+)	-902 bp
Tssr46685	Chr5:75312820-75312847 (+)	-119 bp
Tssr46686	Chr5:75312935-75312958 (+)	-6 bp
Tssr46687	Chr5:75312977-75313028 (+)	50 bp
Tssr46688	Chr5:75314183-75314202 (+)	1,240 bp
Tssr46689	Chr5:75314242-75314270 (+)	1,303 bp
Tssr46690	Chr5:75316098-75316141 (+)	3,167 bp
Tssr46691	Chr5:75316532-75316547 (+)	3,587 bp
Tssr46692	Chr5:75316553-75316580 (+)	3,614 bp
Tssr46693	Chr5:75316608-75316617 (+)	3,660 bp
Tssr46694	Chr5:75324455-75324466 (+)	11,508 bp
Tssr46695	Chr5:75340749-75340769 (+)	27,806 bp
Tssr46696	Chr5:75340771-75340787 (+)	27,826 bp
Tssr46697	Chr5:75340795-75340799 (+)	27,844 bp
Tssr46698	Chr5:75340843-75340854 (+)	27,896 bp

Pdgfra is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Bw8	Chr5, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.
Bw13	Chr5, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.
Bwob	Chr5, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.
Dbsty2	Chr5, 47.29 cM	Chr5:93445064-93445225	J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.
Igfbp3q1	Chr5, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 5, Pdgfra (42 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTLs Dbsty2 (45 cM), Bw8 (42 cM), and Bwob (44 cM) map near this candidate gene. Another candidate gene, Shrm (52 cM), showed differential expression between the restricted and unrestricted diets on the A/a background as well as between A/a and A/A animals on the restricted diet. Diabesity QTL Igfbp3q1 (58 cM) maps near Shrm. Mdh2 (78 cM) shows differential expression between the restricted and unrestricted diets on a A/A background. Diabesity QTL Bw13 (81 cM) maps near candidate gene Mhd2.

*cM position of peak correlated region/marker

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