Pf4 (platelet factor 4) - Rat Genome Database

Name: Pf4
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Pf4 (platelet factor 4) Rattus norvegicus

Analyze

Symbol:

Pf4

Name:

platelet factor 4

RGD ID:

3305

Description:

Predicted to enable CXCR3 chemokine receptor binding activity; chemokine activity; and heparin binding activity. Involved in immune response and protein-containing complex assembly. Located in platelet alpha granule. Part of protein-containing complex. Orthologous to several human genes including PF4 (platelet factor 4); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

C-X-C motif chemokine 4; chemokine (C-X-C motif) ligand 4; Cxcl4; PF-4; Pf4a; RATPF4A

RGD Orthologs

Human

Mouse

Bonobo

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PF4 (platelet factor 4)	HGNC	Ensembl, HomoloGene, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Pf4 (platelet factor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PF4 (platelet factor 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	PF4V1 (platelet factor 4 variant 1)	HGNC	Inparanoid, OrthoDB, Panther, PhylomeDB, Treefam
Alliance orthologs ³
Homo sapiens (human):	PF4 (platelet factor 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Pf4 (platelet factor 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	PF4V1 (platelet factor 4 variant 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	cxcl8b.3 (chemokine (C-X-C motif) ligand 8b, duplicate 3)	Alliance	DIOPT (PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	14	17,298,438 - 17,299,148 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	17,298,308 - 17,299,365 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	17,298,559 - 17,299,267 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	14	18,617,480 - 18,618,188 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	14	17,309,831 - 17,310,539 (-)	NCBI	Rnor_WKY
Rnor_6.0	14	18,848,549 - 18,849,258 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	18,848,549 - 18,849,258 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	18,758,191 - 18,758,900 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	18,812,550 - 18,813,259 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	18,813,312 - 18,815,140 (-)	NCBI
Celera	14	16,674,419 - 16,675,127 (-)	NCBI		Celera
Cytogenetic Map	14	p22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

allergic disease (ISO)

autoimmune disease (ISO)

genetic disease (ISO)

Kabuki Syndrome 1 (ISO)

pneumonia (ISO)

retinal degeneration (IEP)

RETINAL DYSTROPHY WITH INNER RETINAL DYSFUNCTION AND GANGLION CELL ABNORMALITIES (IEP)

thrombocytopenia (ISO)

thrombosis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (EXP)

1-chloro-2,4-dinitrobenzene (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,6-dinitrotoluene (EXP)

2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile (ISO)

2-hydroxypropanoic acid (ISO)

3,3',4,4',5-pentachlorobiphenyl (EXP)

3-isobutyl-1-methyl-7H-xanthine (ISO)

3-methylcholanthrene (ISO)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

4-(ethoxymethylene)-2-phenyloxazol-5-one (ISO)

4-hydroxyphenyl retinamide (ISO)

acetylsalicylic acid (ISO)

acrolein (ISO)

acrylamide (EXP)

ADP (ISO)

aflatoxin B1 (ISO)

aldehydo-D-glucose (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

Aroclor 1254 (ISO)

arsane (ISO)

arsenic atom (ISO)

barium sulfate (EXP)

benzene (ISO)

benzo[a]pyrene (EXP,ISO)

benzoic acid (ISO)

beta-naphthoflavone (EXP)

bexarotene (EXP)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

bucladesine (ISO)

C60 fullerene (EXP)

cangrelor (ISO)

carbon nanotube (ISO)

carbonyl sulfide (EXP)

ceric oxide (EXP)

CGP 52608 (ISO)

choline (ISO)

cisplatin (EXP)

cobalt atom (ISO)

cocaine (ISO)

D-glucose (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

dichloromethane (EXP)

diethyl malate (ISO)

diethylstilbestrol (ISO)

doxorubicin (ISO)

entinostat (ISO)

ethylbenzene (EXP)

flutamide (EXP)

folic acid (ISO)

fructose (ISO)

furan (EXP)

furosemide (EXP)

genistein (ISO)

glucose (ISO)

griseofulvin (ISO)

heparin (ISO)

hydrogen cyanide (ISO)

hydroquinone O-beta-D-glucopyranoside (ISO)

isobutyl nitrite (ISO)

L-methionine (ISO)

lidocaine (EXP)

lipopolysaccharide (ISO)

melatonin (ISO)

methotrexate (ISO)

mifepristone (EXP)

N-nitrosodiethylamine (EXP)

naphthalene (ISO)

neoechinulin A (ISO)

nickel atom (ISO)

nortriptyline (ISO)

ozone (ISO)

paracetamol (ISO)

paroxetine (ISO)

phenformin (EXP)

poly(styrene) (ISO)

potassium cyanide (ISO)

pravastatin (EXP,ISO)

pregnenolone 16alpha-carbonitrile (ISO)

rac-lactic acid (ISO)

rebaudioside A (ISO)

resveratrol (EXP)

sertraline (ISO)

silicon dioxide (EXP,ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

Soman (EXP)

sterigmatocystin (ISO)

steviol (ISO)

stevioside (ISO)

succimer (ISO)

testosterone (ISO)

tetrachloromethane (EXP,ISO)

titanium dioxide (ISO)

toluene 2,4-diisocyanate (ISO)

trichloroethene (EXP)

troglitazone (ISO)

valproic acid (ISO)

verapamil (ISO)

vinclozolin (EXP)

zidovudine (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adenylate cyclase-activating G protein-coupled receptor signaling pathway (ISO,ISS)

antimicrobial humoral immune response mediated by antimicrobial peptide (IBA,ISO)

cellular response to lipopolysaccharide (IBA)

chemokine-mediated signaling pathway (IBA)

cytokine-mediated signaling pathway (ISO,ISS)

defense response to protozoan (ISO)

immune response (IDA)

inflammatory response (IBA)

leukocyte chemotaxis (ISO,ISS)

negative regulation of angiogenesis (ISO,ISS)

negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (ISO)

negative regulation of megakaryocyte differentiation (ISO,ISS)

negative regulation of MHC class II biosynthetic process (ISO)

neutrophil chemotaxis (IBA)

osteoclast differentiation (HEP)

platelet activation (ISO,ISS)

positive regulation of gene expression (ISO)

positive regulation of macrophage derived foam cell differentiation (ISO)

positive regulation of macrophage differentiation (ISO)

positive regulation of transcription by RNA polymerase II (ISO,ISS)

positive regulation of tumor necrosis factor production (ISO)

protein-containing complex assembly (IPI)

regulation of cell population proliferation (ISO,ISS)

response to aldosterone (IEP)

Cellular Component

cytoplasm (ISO)

extracellular space (IBA)

platelet alpha granule (IDA)

protein-containing complex (IDA)

vesicle (IDA)

Molecular Function

chemokine activity (IBA)

CXCR chemokine receptor binding (IBA)

CXCR3 chemokine receptor binding (ISO,ISS)

heparin binding (ISO,ISS)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

chemokine mediated signaling pathway (IEA)

cytokine mediated signaling pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	Immunogold probing of platelet factor 4 in different ploidy classes of rat megakaryocytes sorted by flow cytometry.	Hegyi E, etal., Exp Hematol. 1990 Aug;18(7):789-93.
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	Gene expression changes in the retina after systemic administration of aldosterone.	Ono A, etal., Jpn J Ophthalmol. 2018 Jul;62(4):499-507. doi: 10.1007/s10384-018-0595-4. Epub 2018 Apr 30.
7.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
8.	Biochemical characterization of the serum fetuin-mineral complex.	Price PA, etal., J Biol Chem. 2003 Jun 13;278(24):22153-60. Epub 2003 Apr 3.
9.	Transcriptional regulation of the rat platelet factor 4 gene: interaction between an enhancer/silencer domain and the GATA site.	Ravid K, etal., Mol Cell Biol 1991 Dec;11(12):6116-27.
10.	GOA pipeline	RGD automated data pipeline
11.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
12.	Comprehensive gene review and curation	RGD comprehensive gene curation
13.	Platelet factor 4 fragment induces histamine release from rat peritoneal mast cells.	Suzuki R, etal., Peptides 2002 Oct;23(10):1713-7.
14.	Chemokine and chemokine receptor expression during colony stimulating factor-1-induced osteoclast differentiation in the toothless osteopetrotic rat: a key role for CCL9 (MIP-1gamma) in osteoclastogenesis in vivo and in vitro.	Yang M, etal., Blood. 2006 Mar 15;107(6):2262-70. doi: 10.1182/blood-2005-08-3365. Epub 2005 Nov 22.

Additional References at PubMed

PMID:1688470	PMID:2140694	PMID:3821732	PMID:6945600	PMID:8033893	PMID:9531587	PMID:10666185	PMID:10877842	PMID:11685038	PMID:12041672	PMID:12609849	PMID:12782716
PMID:15187018	PMID:16797058	PMID:17244792	PMID:22206666	PMID:23245326	PMID:28053995

Genomics

Comparative Map Data

Pf4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	14	17,298,438 - 17,299,148 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	17,298,308 - 17,299,365 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	17,298,559 - 17,299,267 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	14	18,617,480 - 18,618,188 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	14	17,309,831 - 17,310,539 (-)	NCBI	Rnor_WKY
Rnor_6.0	14	18,848,549 - 18,849,258 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	18,848,549 - 18,849,258 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	18,758,191 - 18,758,900 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	18,812,550 - 18,813,259 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	18,813,312 - 18,815,140 (-)	NCBI
Celera	14	16,674,419 - 16,675,127 (-)	NCBI		Celera
Cytogenetic Map	14	p22	NCBI

PF4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	73,980,811 - 73,982,124 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	4	73,980,811 - 73,982,027 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	74,846,528 - 74,847,841 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	75,065,660 - 75,066,541 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	4	75,211,830 - 75,212,712	NCBI
Celera	4	72,206,939 - 72,207,858 (-)	NCBI		Celera
Cytogenetic Map	4	q13.3	NCBI
HuRef	4	70,657,501 - 70,658,800 (-)	NCBI		HuRef
CHM1_1	4	74,882,437 - 74,883,736 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	4	77,324,459 - 77,325,772 (-)	NCBI		T2T-CHM13v2.0

Pf4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	90,920,362 - 90,921,242 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	90,920,294 - 90,921,242 (+)	Ensembl		GRCm39 Ensembl
GRCm38	5	90,772,435 - 90,773,383 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	90,772,435 - 90,773,383 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	91,201,461 - 91,202,409 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	91,847,713 - 91,848,583 (+)	NCBI		MGSCv36	mm8
Celera	5	88,924,056 - 88,925,004 (+)	NCBI		Celera
Cytogenetic Map	5	E1	NCBI

PF4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1	4	56,265,831 - 56,267,756 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	50,208,806 - 50,210,570 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	56,041,833 - 56,043,133 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	56,041,833 - 56,043,750 (+)	Ensembl	panpan1.1		panPan2

Variants

Variants in Pf4
3 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	142
Count of miRNA genes:	118
Interacting mature miRNAs:	125
Transcripts:	ENSRNOT00000033406
Prediction methods:	Microtar, Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2300159	Bmd61	Bone mineral density QTL 61	5.3	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	14	1	26541967	Rat
2300183	Bmd60	Bone mineral density QTL 60	5.7	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	14	1	26541967	Rat
619619	Rf4	Renal disease susceptibility QTL 4	4.1	0.002	urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	14	1	32754612	Rat
634352	Apr6	Acute phase response QTL 6	3.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	14	1	41131407	Rat
2293089	Iddm31	Insulin dependent diabetes mellitus QTL 31	4.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	3813074	18274691	Rat
2293089	Iddm31	Insulin dependent diabetes mellitus QTL 31	4.7		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	14	3813074	18274691	Rat
1300114	Srn2	Serum renin concentration QTL 2	3.27		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	14	3813074	21217635	Rat
70195	Mcs8	Mammary carcinoma susceptibility QTL 8	4.28		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	14	3813074	24531477	Rat
1331740	Bw26	Body weight QTL 26	3.028		body mass (VT:0001259)	body weight (CMO:0000012)	14	3813074	30767156	Rat
1581500	Renag1	Renal agenesis QTL 1			kidney development trait (VT:0000527)	percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)	14	8170668	68298175	Rat
1358296	Ael3	Aortic elastin QTL 3	3.7	0.00051	aorta elastin amount (VT:0003905)	aortic elastin	14	8267090	53267090	Rat
2302045	Pia39	Pristane induced arthritis QTL 39	4.9	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G2a level (CMO:0002116)	14	8267090	53267090	Rat
731183	Pia20	Pristane induced arthritis QTL 20	3.55		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	14	9088978	39057237	Rat
2302277	Gluco38	Glucose level QTL 38	5.8		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	11030622	28035204	Rat
631839	Niddm37	Non-insulin dependent diabetes mellitus QTL 37	3.37		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	11030622	95876975	Rat
631212	Bw5	Body weight QTL5	5.43		retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	14	11030812	30320092	Rat
1300140	Srn3	Serum renin concentration QTL 3	3.19		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	14	14875168	30883947	Rat

Markers in Region

D14Wox18

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	17,300,125 - 17,300,272 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	18,850,235 - 18,850,381	NCBI	Rnor6.0
Rnor_5.0	14	18,759,877 - 18,760,023	UniSTS	Rnor5.0
RGSC_v3.4	14	18,814,236 - 18,814,382	UniSTS	RGSC3.4
Celera	14	16,676,104 - 16,676,250	UniSTS
Cytogenetic Map	14	p22	UniSTS

D14Mgh10

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	17,300,069 - 17,300,296 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	18,850,179 - 18,850,405	NCBI	Rnor6.0
Rnor_5.0	14	18,759,821 - 18,760,047	UniSTS	Rnor5.0
RGSC_v3.4	14	18,814,179 - 18,814,406	RGD	RGSC3.4
RGSC_v3.4	14	18,814,180 - 18,814,406	UniSTS	RGSC3.4
RGSC_v3.1	14	18,814,179 - 18,814,406	RGD
Celera	14	16,676,048 - 16,676,274	UniSTS
RH 3.4 Map	14	213.6	UniSTS
RH 3.4 Map	14	213.6	RGD
RH 2.0 Map	14	215.5	RGD
Cytogenetic Map	14	p22	UniSTS

D14Arb3

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	17,299,244 - 17,299,529 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	18,849,355 - 18,849,638	NCBI	Rnor6.0
Rnor_5.0	14	18,758,997 - 18,759,280	UniSTS	Rnor5.0
RGSC_v3.4	14	18,813,355 - 18,813,639	RGD	RGSC3.4
RGSC_v3.4	14	18,813,356 - 18,813,639	UniSTS	RGSC3.4
RGSC_v3.1	14	18,813,355 - 18,813,639	RGD
Celera	14	16,675,224 - 16,675,507	UniSTS
SHRSP x BN Map	14	6.9	UniSTS
SHRSP x BN Map	14	6.9	RGD
Cytogenetic Map	14	p22	UniSTS

RH129105

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	17,298,308 - 17,298,460 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	18,848,420 - 18,848,571	NCBI	Rnor6.0
Rnor_5.0	14	18,758,062 - 18,758,213	UniSTS	Rnor5.0
RGSC_v3.4	14	18,812,421 - 18,812,572	UniSTS	RGSC3.4
Celera	14	16,674,290 - 16,674,441	UniSTS
Cytogenetic Map	14	p22	UniSTS

Pf4

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	17,298,493 - 17,298,715 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	18,848,605 - 18,848,825	NCBI	Rnor6.0
Rnor_5.0	14	18,758,247 - 18,758,467	UniSTS	Rnor5.0
RGSC_v3.4	14	18,812,606 - 18,812,826	UniSTS	RGSC3.4
Celera	14	16,674,475 - 16,674,694	UniSTS
Cytogenetic Map	14	p22	UniSTS

Pf4

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	17,298,700 - 17,299,140 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	18,848,811 - 18,849,250	NCBI	Rnor6.0
Rnor_5.0	14	18,758,453 - 18,758,892	UniSTS	Rnor5.0
RGSC_v3.4	14	18,812,812 - 18,813,251	UniSTS	RGSC3.4
Celera	14	16,674,680 - 16,675,119	UniSTS
Cytogenetic Map	14	p22	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High			4	4		4
Medium	3	41	22	21	12	21	1	2	37	21	32	11	1
Low		2	31	16	7	16	7	9	37	14	9		7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001007729	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH474060	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000250	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M15254	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M83070	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000033406 ⟹ ENSRNOP00000032276

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	14	17,298,308 - 17,299,365 (-)	Ensembl
Rnor_6.0 Ensembl	14	18,848,549 - 18,849,258 (-)	Ensembl

RefSeq Acc Id:

NM_001007729 ⟹ NP_001007730

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	14	17,298,438 - 17,299,148 (-)	NCBI
Rnor_6.0	14	18,848,549 - 18,849,258 (-)	NCBI
Rnor_5.0	14	18,758,191 - 18,758,900 (-)	NCBI
RGSC_v3.4	14	18,812,550 - 18,813,259 (-)	RGD
Celera	14	16,674,419 - 16,675,127 (-)	RGD

Sequence:

show sequence

ATGAGTGCCGCTGCGGTGTTTCGAGGCCTCCGGCCCAGCCCTGAGCTGCTTCTTCTGGGTCTGC
TGTTGCTGCCAGCTGTGGTTGCTGTCACCAGGGCTAGTCCTGAAGAAAGCGACGGAGATCTTAG
CTGTGTGTGTGTGAAGACCAGTTCTTCCAGGATCCATCTCAAACGCATCACCAGCCTGGAGGTG
ATCAAAGCAGGACCCCACTGTGCGGTTCCCCAGCTCATAGCCACGCTGAAGAATGGGAGCAAAA
TTTGCCTGGACCGGCAAGTACCTCTGTATAAGAAAATAATCAAGAAACTCCTGGAGAGTTAG

hide sequence

Protein Sequences


Protein RefSeqs	NP_001007730	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41832	(Get FASTA)	NCBI Sequence Viewer
	EDL88566	(Get FASTA)	NCBI Sequence Viewer
	EDL88567	(Get FASTA)	NCBI Sequence Viewer
	EDL88568	(Get FASTA)	NCBI Sequence Viewer
	P06765	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001007730 ⟸ NM_001007729
- Peptide Label:	precursor
- UniProtKB:	P06765 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MSAAAVFRGLRPSPELLLLGLLLLPAVVAVTRASPEESDGDLSCVCVKTSSSRIHLKRITSLEV IKAGPHCAVPQLIATLKNGSKICLDRQVPLYKKIIKKLLES hide sequence

RefSeq Acc Id:

ENSRNOP00000032276 ⟸ ENSRNOT00000033406

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P06765-F1-model_v2	AlphaFold	P06765	1-105	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13699229

Promoter ID:

EPDNEW_R9752

Type:

multiple initiation site

Name:

Pf4_1

Description:

platelet factor 4

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	14	18,849,331 - 18,849,391	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3305	AgrOrtholog
BioCyc Gene	G2FUF-16205	BioCyc
Ensembl Genes	ENSRNOG00000028015	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000032276	ENTREZGENE
	ENSRNOP00000032276.1	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000033406	ENTREZGENE
	ENSRNOT00000033406.2	UniProtKB/Swiss-Prot
Gene3D-CATH	2.40.50.40	UniProtKB/Swiss-Prot
InterPro	Chemokine_CXC	UniProtKB/Swiss-Prot
	Chemokine_CXC_CS	UniProtKB/Swiss-Prot
	Chemokine_IL8-like_dom	UniProtKB/Swiss-Prot
	CXC_Chemokine_domain	UniProtKB/Swiss-Prot
	Interleukin_8-like_sf	UniProtKB/Swiss-Prot
KEGG Report	rno:360918	UniProtKB/Swiss-Prot
NCBI Gene	360918	ENTREZGENE
PANTHER	PTHR10179	UniProtKB/Swiss-Prot
	PTHR10179:SF43	UniProtKB/Swiss-Prot
Pfam	IL8	UniProtKB/Swiss-Prot
PhenoGen	Pf4	PhenoGen
PRINTS	INTERLEUKIN8	UniProtKB/Swiss-Prot
	SMALLCYTKCXC	UniProtKB/Swiss-Prot
PROSITE	SMALL_CYTOKINES_CXC	UniProtKB/Swiss-Prot
SMART	SCY	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF54117	UniProtKB/Swiss-Prot
UniProt	P06765	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-19	Pf4	platelet factor 4	Cxcl4	chemokine (C-X-C motif) ligand 4	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Cxcl4	chemokine (C-X-C motif) ligand 4	Pf4	platelet factor 4	Symbol and Name updated	1299863	APPROVED
2002-06-10	Pf4	Platelet factor 4			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_process	induces histamine release from peritoneal mast cells	724612

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)