Ptx4 (pentraxin 4) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Ptx4 (pentraxin 4) Rattus norvegicus
Analyze
Symbol: Ptx4
Name: pentraxin 4
RGD ID: 1311190
Description: Orthologous to human PTX4 (pentraxin 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; arsane (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC287130; pentraxin 4, long; pentraxin-4; RGD1311190; similar to Neuronal pentraxin II precursor (NP-II) (NP2) (Neuronal activity-regulated pentraxin)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81014,644,501 - 14,650,185 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1014,644,551 - 14,649,698 (+)EnsemblGRCr8
mRatBN7.21014,140,028 - 14,146,163 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,140,304 - 14,144,846 (+)EnsemblmRatBN7.2
Rnor_6.01014,481,044 - 14,486,277 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1014,481,393 - 14,485,916 (+)Ensemblrn6Rnor6.0
Rnor_5.01014,296,757 - 14,301,718 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41014,368,352 - 14,372,875 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1013,812,631 - 13,817,866 (+)NCBICelera
RGSC_v3.11014,368,351 - 14,372,875 (+)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20223226  


Genomics

Comparative Map Data
Ptx4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81014,644,501 - 14,650,185 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1014,644,551 - 14,649,698 (+)EnsemblGRCr8
mRatBN7.21014,140,028 - 14,146,163 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,140,304 - 14,144,846 (+)EnsemblmRatBN7.2
Rnor_6.01014,481,044 - 14,486,277 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1014,481,393 - 14,485,916 (+)Ensemblrn6Rnor6.0
Rnor_5.01014,296,757 - 14,301,718 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41014,368,352 - 14,372,875 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1013,812,631 - 13,817,866 (+)NCBICelera
RGSC_v3.11014,368,351 - 14,372,875 (+)NCBI
Cytogenetic Map10q12NCBI
PTX4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38161,485,886 - 1,488,944 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl161,485,886 - 1,488,981 (-)Ensemblhg38GRCh38
GRCh37161,535,887 - 1,538,945 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36161,475,941 - 1,478,469 (-)NCBIBuild 36Build 36hg18NCBI36
Celera161,748,221 - 1,750,749 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef161,461,875 - 1,464,403 (-)NCBIHuRef
CHM1_1161,535,936 - 1,538,464 (-)NCBICHM1_1
T2T-CHM13v2.0161,500,922 - 1,503,980 (-)NCBIT2T-CHM13v2.0
Ptx4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391725,339,328 - 25,344,256 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1725,339,734 - 25,344,266 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381725,120,697 - 25,125,293 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1725,120,760 - 25,125,292 (+)Ensemblmm10GRCm38
MGSCv371725,257,705 - 25,262,213 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361724,848,360 - 24,852,868 (+)NCBIMGSCv36mm8
Celera1725,649,343 - 25,653,851 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.53NCBI
Ptx4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544215,752,957 - 15,756,801 (+)Ensembl
ChiLan1.0NW_00495544215,750,881 - 15,757,906 (+)NCBIChiLan1.0ChiLan1.0
PTX4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2181,745,644 - 1,751,548 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1165,532,974 - 5,538,821 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v016105,005 - 113,730 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1161,540,411 - 1,543,522 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl161,540,411 - 1,543,413 (-)EnsemblpanPan2panpan1.1
PTX4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1639,320,647 - 39,328,256 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl639,322,920 - 39,327,711 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha640,590,542 - 40,595,951 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0639,668,577 - 39,673,986 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl639,669,213 - 39,673,132 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1639,345,687 - 39,351,096 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0639,317,861 - 39,323,270 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0639,796,614 - 39,802,024 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ptx4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344104,269,796 - 104,274,202 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366942,436,755 - 2,441,802 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366942,435,291 - 2,439,837 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTX4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl340,382,667 - 40,390,812 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1340,383,325 - 40,391,567 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2341,846,547 - 41,854,720 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTX4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.151,394,909 - 1,404,015 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl51,395,234 - 1,398,238 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606829,682,743 - 29,691,894 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ptx4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624913736,680 - 739,342 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624913732,810 - 742,648 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ptx4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v192,389,221 - 2,393,575 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ptx4
17 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:21
Count of miRNA genes:20
Interacting mature miRNAs:21
Transcripts:ENSRNOT00000022697
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat

Markers in Region
D10Got28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21014,139,471 - 14,139,683 (+)MAPPERmRatBN7.2
Rnor_6.01014,480,561 - 14,480,772NCBIRnor6.0
Rnor_5.01014,295,992 - 14,296,203UniSTSRnor5.0
RGSC_v3.41014,367,519 - 14,367,731RGDRGSC3.4
RGSC_v3.41014,367,520 - 14,367,731UniSTSRGSC3.4
Celera1013,812,148 - 13,812,359UniSTS
RGSC_v3.11014,367,520 - 14,367,731RGD
RH 3.4 Map10165.4UniSTS
RH 3.4 Map10165.4RGD
RH 2.0 Map10128.0RGD
Cytogenetic Map10q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
1 11 42 67 8 9 24 6 123 85 11 52 30 29 9 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000091072   ⟹   ENSRNOP00000070878
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1014,644,551 - 14,649,698 (+)Ensembl
mRatBN7.2 Ensembl1014,140,304 - 14,144,846 (+)Ensembl
Rnor_6.0 Ensembl1014,481,393 - 14,485,916 (+)Ensembl
RefSeq Acc Id: XM_220237   ⟹   XP_220237
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,644,501 - 14,650,185 (+)NCBI
mRatBN7.21014,140,028 - 14,146,163 (+)NCBI
Rnor_6.01014,481,044 - 14,486,277 (+)NCBI
Rnor_5.01014,296,757 - 14,301,718 (+)NCBI
RGSC_v3.41014,368,352 - 14,372,875 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_220237 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03903 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000070878
  ENSRNOP00000070878.3
RefSeq Acc Id: XP_220237   ⟸   XM_220237
- UniProtKB: A0A0G2JZ18 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000070878   ⟸   ENSRNOT00000091072

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JZ18-F1-model_v2 AlphaFold A0A0G2JZ18 1-478 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311190 AgrOrtholog
BioCyc Gene G2FUF-25806 BioCyc
Ensembl Genes ENSRNOG00000060934 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000091072 ENTREZGENE
  ENSRNOT00000091072.3 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.200 UniProtKB/TrEMBL
InterPro ConA-like_subgrp UniProtKB/TrEMBL
  Neuronal_Pentraxin_Related UniProtKB/TrEMBL
  Pentaxin UniProtKB/TrEMBL
NCBI Gene 287130 ENTREZGENE
PANTHER PENTRAXIN UniProtKB/TrEMBL
  PENTRAXIN-4 UniProtKB/TrEMBL
Pfam Pentaxin UniProtKB/TrEMBL
PhenoGen Ptx4 PhenoGen
PRINTS PENTAXIN UniProtKB/TrEMBL
PROSITE PTX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000060934 RatGTEx
SMART PTX UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
UniProt A0A0G2JZ18 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Ptx4  pentraxin 4  Ptx4  pentraxin 4, long  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-05-13 Ptx4  pentraxin 4, long  RGD1311190  similar to Neuronal pentraxin II precursor (NP-II) (NP2) (Neuronal activity-regulated pentraxin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1311190  similar to Neuronal pentraxin II precursor (NP-II) (NP2) (Neuronal activity-regulated pentraxin)   RGD1311190_predicted  similar to Neuronal pentraxin II precursor (NP-II) (NP2) (Neuronal activity-regulated pentraxin) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1311190_predicted  similar to Neuronal pentraxin II precursor (NP-II) (NP2) (Neuronal activity-regulated pentraxin) (predicted)  LOC287130_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287130_predicted  similar to Neuronal pentraxin II precursor (NP-II) (NP2) (Neuronal activity-regulated pentraxin) (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL