PTX3 (pentraxin 3) - Rat Genome Database

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

Gene: PTX3 (pentraxin 3) Chlorocebus sabaeus

Analyze

Symbol:

PTX3

Name:

pentraxin 3

RGD ID:

18515945

Description:

ENCODES a protein that exhibits (1->3)-beta-D-glucan binding (inferred); complement component C1q complex binding (inferred); identical protein binding (inferred); INVOLVED IN extracellular matrix organization (ortholog); opsonization (ortholog); ovarian cumulus expansion (ortholog); ASSOCIATED WITH Arsenic Poisoning (ortholog); cystic fibrosis (ortholog); Diabetic Foot (ortholog); FOUND IN extracellular matrix (inferred); extracellular space (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

pentraxin-related protein PTX3

RGD Orthologs

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)	NCBI	Ortholog
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
Sus scrofa (pig):	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:

ChlSab1.1 - Green Monkey 1.1 Assembly

Position:

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	15	33,320,592 - 33,327,236 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	15	33,321,208 - 33,327,268 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666041	5,897,822 - 5,904,486 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

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)

genetic disease (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 Ontology Annotations Click to see Annotation Detail View

Biological Process

extracellular matrix organization (IEA,ISO)

immune response (IEA)

innate immune response (IEA)

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 (IEA)

negative regulation of glycoprotein metabolic process (IEA)

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 (IEA)

Molecular Function

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

complement component C1q complex binding (IEA)

identical protein binding (IEA)

protein binding (ISO)

virion binding (IEA)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

PTX3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	15	33,320,592 - 33,327,236 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	15	33,321,208 - 33,327,268 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666041	5,897,822 - 5,904,486 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

PTX3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	157,436,850 - 157,443,633 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	157,436,850 - 157,443,633 (+)	Ensembl	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	Build 36	hg18	NCBI36
Build 34	3	158,637,308 - 158,644,078	NCBI
Celera	3	155,578,255 - 155,585,092 (+)	NCBI		Celera
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
T2T-CHM13v2.0	3	160,211,418 - 160,218,201 (+)	NCBI		T2T-CHM13v2.0

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	GRCm39	mm39
GRCm39 Ensembl	3	66,127,331 - 66,133,226 (+)	Ensembl		GRCm39 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	MGSCv37	mm9	NCBIm37
MGSCv36	3	66,307,812 - 66,313,734 (+)	NCBI		MGSCv36	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
GRCr8	2	152,797,563 - 152,803,372 (+)	NCBI		GRCr8
mRatBN7.2	2	150,487,513 - 150,493,323 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	150,487,513 - 150,493,323 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	2	157,593,206 - 157,599,014 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	155,643,731 - 155,649,539 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	150,276,449 - 150,282,257 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	158,097,843 - 158,103,653 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	158,097,843 - 158,103,653 (+)	Ensembl	Rnor6.0		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	RGSC_v3.4	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
NHGRI_mPanPan1-v2	2	155,347,564 - 155,354,440 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	155,347,508 - 155,359,171 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	154,485,470 - 154,492,293 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
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

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		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	23	51,586,874 - 51,592,673 (+)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	23	51,169,291 - 51,175,068 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	23	51,222,224 - 51,228,028 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	23	51,507,584 - 51,513,394 (+)	NCBI		UU_Cfam_GSD_1.0

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		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936519	4,303,464 - 4,309,173 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936519	4,303,549 - 4,309,143 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

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
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624730	35,125,605 - 35,131,367 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624730	35,125,536 - 35,131,645 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

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

	endocrine system	hemolymphoid system	nervous system
High
Medium
Low	34	15	34
Below cutoff	2	5	26

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_008008587	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000009	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCSAT00000010173 ⟹ ENSCSAP00000008268

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	15	33,321,208 - 33,327,268 (-)	Ensembl

RefSeq Acc Id:

XM_008008587 ⟹ XP_008006778

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	15	33,320,592 - 33,327,236 (-)	NCBI
Vero_WHO_p1.0	NW_023666041	5,897,822 - 5,904,486 (-)	NCBI

Sequence:

show sequence

TCCCCATTCAGGCTTTTCCCCAGCATTTATTAAGGGCTCTCTGCTCCAGCCTCTCACTCTCATT
CTCCTCCGCTCAAATTCAGCTCACTTGAGAGTCTCCTCCCGCCAGCTGTGGAAAGAACTTTGCG
TCTCTCCAGCAATGCATCTTCTTGCGATTCTGTTTTGTGCTCTCTGGTCTGCAGTGTTGGCCGA
GAACTCGGATGATTATGATCTCATGTATGTGAATTTGGACAACGAAATAGACAATGGACTCCAT
CCCACTGAGGACCCCACGCCGTGCGACTGCCGTCAGGAACACTCCGAATGGGACAAGCTCTTCA
TCATGCTGGAGAACTCGCAGATGAGAGAGGGCATGCTGCTGCAAGCCACGGACGACGTCCTGCG
GGGCGAGCTGCAGAGGCTGCGGGAGGAGCTGGGCCGGCTAGCGGAAAGCCTGGCGAGGCCATGC
GAGCAGGGAGCTCTCGCGGAGGCCAAGCTGGCTAGCGCTCTGGACGAGCTGCTGCAGGCGAGCC
GCGACGCGGGCCGCAGGCTGGAGCGCCTGGAGGGCGCGGAGACGCAGCGCCCAGAGGAGGCGGG
GCGCGCCCTGGCCGCGATGCTGGAGGAGCTGAGGCAGACGCGAGCCGACCTGCACGCAGTGCAG
GGCTGGGCGGCCCGGACCTGGCTGCCGGCAGGTTGTGAAACAGCTATTTTATTCCCAATGCGTT
CCAAGAAGATTTTTGGAAGCGTGCATCCAGTGAGACCAATGAGGCTTGAATCTTTCAGTGCCTG
CATTTGGGTCAAAGCCACAGATGTGTTAAACAAAACCATCCTGTTTTCCTATGGCACAAAGAGG
AATCCATATGAAATCCAGCTGTATCTCAGCTACCAGTCCATAGTGTTTGTGGTGGGTGGAGAGG
AAAACAAACTGGTTGCTGAAACCATGGTTTCCCTGGGAAGGTGGACCCACCTGTGCAGCACCTG
GAATTCAGAGAAAGGGCTCACATCCTTGTGGGTAAATGGTGAACTGGTGGCTACCACTGTTGAG
ATGGCCACAGGTCACACTGTTCCTGAGGGAGGAATCCTGCAGATTGGCCAAGAAAAGAATGGCT
GCTGTGTGGGTGGTGGCTTTGATGAAACATTAGCCTTCTCTGGGAGACTCACAGGCTTCAATAT
CTGGGATAGTGTTCTTAGCAATGAAGAGATAAGAGAGACTGGAGGAGCAGAGTCTTGTCACATC
CGGGGGAATATTGTTGGATGGGGAGTTACAGAGATCCAGCCACATGGAGGAGCTCAGTATGTTT
CATAAGTGTTGTGAAACTCCACGTGAAGCCAAAGAAAGAAACTCACACTTAAAATACATGCCAG
TTGGGAAGGTCTGAAAACTTAATGCATAATAGGAACACTTGAGACTAATGAAGGAGAGAGTTGA
GATCAATCTTTATTTGTACTGGCAAAATAGTGAATAAACAGTTGAAGGAAAGACATTGGAAAAA
GCTTTTGAGGATAATGTTACTAGACTTTATGCCATGGTGCTTTCAGTTTAATGCTGTGTCTCTG
TCAGATAAACTCTCAAATAATTAAAAAGGACTGTATTGTTGAACAGAAGGACAATTGTTTTACT
TTTCTTTGGTTAACTTTGTTTTGGCCAGAGATTAATTTTACATTGGAAGAATAACAAAATAAGA
TTTGTTGTCCACTGTTCATTGTTATTGGTGTGTACCTTATTACAAAAAAAAGATGATGAAAACA
TATTTATACTACAAGGTGGCTTAACAACTATAAATGTAGTTTATGTGTTGTAATCGAATGTCAC
TTTTTTGAGAAGATAGTCATATAAGTTATATTGTAAAAGGGATTTGTATTAATTTTATTAAGAC
TATTTTTGTAAAGCTCTACTGTAAATAAAATGTTTTATAAAACTA

hide sequence

Protein Sequences


Protein RefSeqs	XP_008006778	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000008268
	ENSCSAP00000008268.1

RefSeq Acc Id:	XP_008006778 ⟸ XM_008008587
- UniProtKB:	A0A0D9RI29 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSCSAP00000008268 ⟸ ENSCSAT00000010173

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000012090	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000010173.1	UniProtKB/TrEMBL
Gene3D-CATH	2.60.120.200	UniProtKB/TrEMBL
InterPro	ConA-like_dom_sf	UniProtKB/TrEMBL
	LamG-like	UniProtKB/TrEMBL
	Pentaxin_CS	UniProtKB/TrEMBL
	Pentraxin-related	UniProtKB/TrEMBL
	PTX3	UniProtKB/TrEMBL
KEGG Report	csab:103241420	UniProtKB/TrEMBL
NCBI Gene	PTX3	ENTREZGENE
PANTHER	PENTRAXIN-RELATED PROTEIN PTX3	UniProtKB/TrEMBL
	PTHR46943	UniProtKB/TrEMBL
Pfam	Pentaxin	UniProtKB/TrEMBL
PRINTS	PENTAXIN	UniProtKB/TrEMBL
PROSITE	PTX_1	UniProtKB/TrEMBL
	PTX_2	UniProtKB/TrEMBL
SMART	LamGL	UniProtKB/TrEMBL
	PTX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF49899	UniProtKB/TrEMBL
UniProt	A0A0D9RI29	ENTREZGENE, UniProtKB/TrEMBL

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)

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