PTX3 (pentraxin 3) - Rat Genome Database

Name: PTX3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: PTX3 (pentraxin 3) Sus scrofa

Analyze

Symbol:

PTX3

Name:

pentraxin 3

RGD ID:

14248854

Description:

ENCODES a protein that exhibits (1->3)-beta-D-glucan binding (inferred); identical protein binding (inferred); virion binding (inferred); INVOLVED IN extracellular matrix organization (ortholog); negative regulation of exo-alpha-sialidase activity (ortholog); negative regulation of glycoprotein metabolic process (ortholog); ASSOCIATED WITH Arsenic Poisoning (ortholog); cystic fibrosis (ortholog); Diabetic Foot (ortholog); FOUND IN extracellular space (ortholog); INTERACTS WITH N-acetyl-L-cysteine; zearalenone

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

pentraxin 3, long; pentraxin-related protein PTX3; PTX-3

RGD Orthologs

Human

Mouse

Rat

Chinchilla

Bonobo

Dog

Squirrel

Green Monkey

Naked Mole-Rat

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):	PTX3 (pentraxin 3)	HGNC	EggNOG, Ensembl, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Ptx3 (pentraxin related gene)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Ptx3 (pentraxin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Ptx3 (pentraxin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PTX3 (pentraxin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PTX3 (pentraxin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ptx3 (pentraxin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PTX3 (pentraxin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ptx3 (pentraxin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	97,273,594 - 97,279,569 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	97,273,594 - 97,279,570 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	105,440,917 - 105,446,892 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Arsenic Poisoning (ISO)

cystic fibrosis (ISO)

Diabetic Foot (ISO)

hepatitis C (ISO)

invasive aspergillosis (ISO)

Invasive Candidiasis (ISO)

Invasive Fungal Infections (ISO)

Invasive Pulmonary Aspergillosis (ISO)

necrotizing soft tissue infection (ISO)

pelvic inflammatory disease (ISO)

Pseudomonas Infections (ISO)

pulmonary aspergilloma (ISO)

pulmonary fibrosis (ISO)

skin disease (ISO)

toxic shock syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

N-acetyl-L-cysteine (EXP)

zearalenone (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

extracellular matrix organization (IEA,ISO)

innate immune response (IBA)

negative regulation by host of viral exo-alpha-sialidase activity (IEA)

negative regulation by host of viral glycoprotein metabolic process (IEA)

negative regulation by host of viral process (IBA)

negative regulation of exo-alpha-sialidase activity (ISO)

negative regulation of glycoprotein metabolic process (ISO)

negative regulation of viral entry into host cell (IEA)

opsonization (IEA,ISO)

ovarian cumulus expansion (IEA,ISO)

positive regulation of nitric oxide biosynthetic process (IEA,ISO)

positive regulation of phagocytosis (IEA,ISO)

response to yeast (IEA,ISO)

Cellular Component

extracellular matrix (IEA)

extracellular space (IBA,ISO)

Molecular Function

(1->3)-beta-D-glucan binding (IEA)

complement component C1q complex binding (IBA)

identical protein binding (IEA)

protein binding (ISO)

virion binding (IEA)

References

Additional References at PubMed

PMID:14681463	PMID:22120828	PMID:28039065

Genomics

Comparative Map Data

PTX3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	97,273,594 - 97,279,569 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	97,273,594 - 97,279,570 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	105,440,917 - 105,446,892 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PTX3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	3	157,436,850 - 157,443,633 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	3	157,436,850 - 157,443,633 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	3	157,154,639 - 157,161,422 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	158,637,301 - 158,644,071 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	3	158,637,308 - 158,644,078	NCBI
Celera	3	155,578,255 - 155,585,092 (+)	NCBI
Cytogenetic Map	3	q25.32	NCBI
HuRef	3	154,550,694 - 154,557,531 (+)	NCBI		HuRef
CHM1_1	3	157,117,566 - 157,124,403 (+)	NCBI		CHM1_1

Ptx3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	66,127,308 - 66,133,227 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	3	66,127,331 - 66,133,226 (+)	Ensembl
GRCm38	3	66,219,887 - 66,225,806 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	66,219,910 - 66,225,805 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	66,023,809 - 66,029,728 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	3	66,307,812 - 66,313,734 (+)	NCBI			mm8
Celera	3	66,363,920 - 66,369,839 (+)	NCBI		Celera
Cytogenetic Map	3	E1	NCBI
cM Map	3	30.25	NCBI

Ptx3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	2	150,487,513 - 150,493,323 (+)	NCBI
Rnor_6.0 Ensembl	2	158,097,843 - 158,103,653 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	158,097,843 - 158,103,653 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	2	177,457,263 - 177,463,073 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	156,089,917 - 156,095,726 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	2	144,894,946 - 144,900,755 (+)	NCBI		Celera
Cytogenetic Map	2	q31	NCBI

Ptx3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955448	8,366,925 - 8,372,411 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955448	8,366,795 - 8,373,010 (+)	NCBI	ChiLan1.0	ChiLan1.0

PTX3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	3	162,537,440 - 162,544,263 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	162,537,577 - 162,543,652 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	3	154,485,470 - 154,492,293 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

PTX3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	23	50,952,835 - 50,958,607 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	23	50,952,885 - 50,958,167 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	23	50,825,322 - 50,831,079 (+)	NCBI
ROS_Cfam_1.0	23	51,586,874 - 51,592,673 (+)	NCBI
UMICH_Zoey_3.1	23	51,169,291 - 51,175,068 (+)	NCBI
UNSW_CanFamBas_1.0	23	51,222,224 - 51,228,028 (+)	NCBI
UU_Cfam_GSD_1.0	23	51,507,584 - 51,513,394 (+)	NCBI

Ptx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405602	85,424,779 - 85,430,719 (-)	NCBI
SpeTri2.0	NW_004936519	4,303,549 - 4,309,143 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PTX3
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	15	33,320,592 - 33,327,236 (-)	NCBI
ChlSab1.1 Ensembl	15	33,321,208 - 33,327,268 (-)	Ensembl

Ptx3
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624730	35,125,536 - 35,131,645 (+)	NCBI

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	hemolymphoid system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system
High
Medium								1
Low	9	1	3	1	2	19	2	2
Below cutoff	1	3		3		4			1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001244783	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000089	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK236052	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CU633549	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GFLN01090957	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GQ412351	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KT861480	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSSSCT00000012837 ⟹ ENSSSCP00000012497

RefSeq Status:

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1 Ensembl	13	97,273,594 - 97,279,569 (+)	Ensembl

RefSeq Acc Id:

NM_001244783 ⟹ NP_001231712

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	13	97,273,594 - 97,279,570 (+)	NCBI

Sequence:

show sequence

AGCATTTATTAAGGGCTCTCAGCTCCTGCCTCTCACTCTCACTCTCCTCTGGCTCCTTCTCTGT
TCATTTGAAAGCCTCTTGCCTCACACCCTCCCGCCAGCTGTGGGAAGAACTTTTGTCTCTTCAG
CAATGCGTCTCCCAGCGATTCTGTTTTGTGCTCTCTGGTCTGCAGTGTTGGCCGAGAACTCCGA
TGATTATGAGCTCATGTATGTGAATTTGGACAACGAGATAGACAATGGACTCCATCCCACTGAG
GACCCCACGCTGTGCGACTGCAGTCCAGAGCACTCTGAGTGGGACAAGCTCTTCATCATGCTAG
AGAACTCCCAGATGCGGGAGAGCATGCTTCTGCAGGCCACCGATGACATCCTCCGGGGCGAACT
GCAGAGGCTGAGGGCCGAGCTGGGGCGGCTGGCAGGCAGCCTGGCGAGGCCTTGCGCACCGACA
GCCCCAGCGGAGGTCCAGTTGGCCCGGGCGCTGGACGAGCTGCTGCAGGCGAGCCGCGACGCTG
GCCGCAGGCTGGAGCGCCTAGAGGAAGCTGGGACTCCGCAGCTGCAGGAGGAGGCGGGGCGGAC
CCTGGGCGCGGTGCTCGAGGAGCTGAGGCGGACGCGGGCTGACCTCCGTGCAGTGCAGGGCTGG
GCCGCGGGGCGCTGGCTGCCAGCAGGTTGTGAAACAGCGATTTTATTCCCCATGCGTTCCAAGA
AGATTTTTGCAAGTGTGCACCCGGCAACACCAATGAAACTTGAGGCTTTCAGTGCCTGCATTTG
GGTCAAAGCCACAGATGTACTGAGCAAAACCATCCTGTTTTCCTATGGCACAAAGAGGAATCCA
TATGAGATCCAGCTGTACCTCAGCTATCAGTCCACTGTGCTTGTGGTGGGGGGAGAGGAAAACA
GACTGGTCGCCAATACTGTGATTTCCCCTGGAACGTGGACCCATCTGTGCAGCACCTGGAATTC
TGAACAAGGGCATGTAGCCTTGTGGGTCAACGGTGACCTGATAGCCACCAAGGTCGACATGGCC
ACGGGTCACATTGTTCCAGGAGGAGGAATCCTGCAGATTGGCCAAGAAAAGAATGGATGCTGTG
TGGGTGGTGGCTTTGATGAAATATTAGCCTTTTCTGGAAGACTCACAGGCTTCAATATCTGGGA
TCGTGTTCTCAGCACCGAAGAGATAAAAAAGACTGGAGGAGCAGAGTCCTGTCACATCCGGGGG
AATGTGGTTGGGTGGGGAGTCACAGAGATTCAGCCCCATGGAGGAGCTCAATACGTTTCTTAAG
TGTTGTGAAACTCTACTCGGAGCCAAAGAAAGAAACTCACATTTTAAACATTTGGGAAGGTCTA
AAAACTTTGATGCATATTAAGAACACTTGAGACTAATGAAGGAGAGAGTTGAGATCAATCTTTA
TTTATCTTGGCAAAATACTGGGCAAAGAGTGGAAGGGGAGACATTGGAGAAGGCTTTGGGGTAT
ACTGTTACTAGACTTTATGCCATGGTGCTTTCAGATTAATGCTGTGTCTTTGTCAGATAAATTC
TCAAATAATTAAAAAGGACTGTGTGGTTGAACAGAAGGATAATTGTTTCACTTCTCTTTGGTTA
ATTTTGTTTTGGCCAGGGATGAATTTTACATTGAAAGAATAATAAAATAACACATGTTGTTCAT
TGCTCACTGTCATTGGTATATACCTTATTACAAAAAATGATGATAAAACATATTTATGCTACAA
AGTGACTTAACAAATACAAATGTAGTTTATGTGTTATAATCAAATGTCACTTGTTGGAGAGGAT
AGCTATATAAGTTATACTGTAAAATGGTTTTGTATTAATTTTATTAAGACTATTTTTATAAAGC
TCTACTATAAATAAAATATTTTATAAAACTAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001231712	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	ANJ46799	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001231712 ⟸ NM_001244783

- Peptide Label:

precursor

- Sequence:

show sequence

MRLPAILFCALWSAVLAENSDDYELMYVNLDNEIDNGLHPTEDPTLCDCSPEHSEWDKLFIMLE
NSQMRESMLLQATDDILRGELQRLRAELGRLAGSLARPCAPTAPAEVQLARALDELLQASRDAG
RRLERLEEAGTPQLQEEAGRTLGAVLEELRRTRADLRAVQGWAAGRWLPAGCETAILFPMRSKK
IFASVHPATPMKLEAFSACIWVKATDVLSKTILFSYGTKRNPYEIQLYLSYQSTVLVVGGEENR
LVANTVISPGTWTHLCSTWNSEQGHVALWVNGDLIATKVDMATGHIVPGGGILQIGQEKNGCCV
GGGFDEILAFSGRLTGFNIWDRVLSTEEIKKTGGAESCHIRGNVVGWGVTEIQPHGGAQYVS

hide sequence

RefSeq Acc Id:

ENSSSCP00000012497 ⟸ ENSSSCT00000012837

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00000011727	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCG00070001481	UniProtKB/TrEMBL
Ensembl Protein	ENSSSCP00000012497	ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCP00070002304	UniProtKB/TrEMBL
	ENSSSCP00070002312	UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00000012837	ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCT00070002787	UniProtKB/TrEMBL
	ENSSSCT00070002796	UniProtKB/TrEMBL
InterPro	ConA-like_dom_sf	UniProtKB/TrEMBL
	Pentaxin_CS	UniProtKB/TrEMBL
	Pentraxin-related	UniProtKB/TrEMBL
	PTX3	UniProtKB/TrEMBL
NCBI Gene	PTX3	ENTREZGENE
PANTHER	PTHR46943	UniProtKB/TrEMBL
Pfam	Pentaxin	UniProtKB/TrEMBL
PRINTS	PENTAXIN	UniProtKB/TrEMBL
PROSITE	PTX_1	UniProtKB/TrEMBL
	PTX_2	UniProtKB/TrEMBL
SMART	PTX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF49899	UniProtKB/TrEMBL
UniProt	A0A4X1SJS5_PIG	UniProtKB/TrEMBL
	A0A4X1SK74_PIG	UniProtKB/TrEMBL
	F1SJM0_PIG	UniProtKB/TrEMBL
VGNC ID	VGNC:92000	ENTREZGENE

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

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