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NPTXR Gene

protein-coding GIFtS: 56
GCID: GC22M039214

Neuronal Pentraxin Receptor

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
Neuronal Pentraxin Receptor¹ ²
NPR²

External Ids:	HGNC: 7954¹	Entrez Gene: 23467²	Ensembl: ENSG00000221890⁷	OMIM: 609474⁵	UniProtKB: O95502³

Export aliases for NPTXR gene to outside databases

Previous GC identifers: GC22M035828 GC22M037457 GC22M037538 GC22M022180

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for NPTXR Gene:

This gene encodes a protein similar to the rat neuronal pentraxin receptor. The rat pentraxin receptor is an

integral membrane protein that is thought to mediate neuronal uptake of the snake venom toxin, taipoxin, and its

transport into the synapses. Studies in rat indicate that translation of this mRNA initiates at a non-AUG (CUG)

codon. This may also be true for mouse and human, based on strong sequence conservation amongst these species.

(provided by RefSeq, Jul 2008)

GeneCards Summary for NPTXR Gene:

NPTXR (neuronal pentraxin receptor) is a protein-coding gene. An important paralog of this gene is NPTX2.

UniProtKB/Swiss-Prot: NPTXR_HUMAN, O95502

Function: May be involved in mediating uptake of synaptic material during synapse remodeling or in mediating the

synaptic clustering of AMPA glutamate receptors at a subset of excitatory synapses (By similarity)

Gene Wiki entry for NPTXR Gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:

NC_000022.10 NC_018933.2 NT_011520.13

Regulatory elements:

Regulatory transcription factor binding sites in the NPTXR gene promoter:
HOXA9 HOXA9B AML1a Pax-5 Lmo2 AP-4 Evi-1 Meis-1b HOXA5 Meis-1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: NPTXR promoter sequence

Search Chromatin IP Primers for NPTXR

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NPTXR

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q13.1 Ensembl cytogenetic band: 22q13.1 HGNC cytogenetic band: 22q13.1

NPTXR Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NPTXR gene location

GeneLoc information about chromosome 22 GeneLoc Exon Structure

GeneLoc location for GC22M039214: view genomic region (about GC identifiers)

Start:	39,214,456 bp from pter	End:	39,240,017 bp from pter
Size:	25,562 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: NPTXR_HUMAN, O95502 (See protein sequence)

Recommended Name: Neuronal pentraxin receptor

Size: 500 amino acids; 52846 Da

Cofactor: Binds 2 calcium ions per subunit (By similarity)

Subunit: Heteropentamer with NPTX1 and/or NPTX2. Also binds taipoxin-associated calcium-binding protein 49

(TCBP49/RCN2). Interacts with KLHL2 (By similarity)

Sequence caution: Sequence=CAA15430.3; Type=Erroneous gene model prediction;

Explore the universe of human proteins at neXtProt for NPTXR: NX_O95502

Explore proteomics data for NPTXR at MOPED

Post-translational modifications:

Ubiquitinated by a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex containing KLHL2 (By

similarity)¹

Glycosylation² at Asn42, Asn216, Asn463

See NPTXR Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_055108.2

ENSEMBL proteins:

ENSP00000327545

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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3 InterPro protein domains:

IPR013320 ConA-like_subgrp

IPR001759 Pentaxin

IPR008985 ConA-like_lec_gl_sf

Graphical View of Domain Structure for InterPro Entry O95502

ProtoNet protein and cluster: O95502

1 Blocks protein domain: IPB001759 Pentaxin

UniProtKB/Swiss-Prot: NPTXR_HUMAN, O95502

Similarity: Contains 1 pentaxin domain

Find genes that share domains with NPTXR About GenesLikeMe

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: NPTXR_HUMAN, O95502

Function: May be involved in mediating uptake of synaptic material during synapse remodeling or in mediating the

synaptic clustering of AMPA glutamate receptors at a subset of excitatory synapses (By similarity)

Genatlas biochemistry entry for NPTXR:

neuronal pentraxin receptor,interacting with NPTX1,NPTX2 and taipoxin-associated calcium binding protein

49,putatively involved in the clearance of synaptic debris

Gene Ontology (GO): 1 molecular function term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0046872	metal ion binding	IEA	--

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Phenotypes:
1 MGI mutant phenotype (inferred from 1 allele) (MGI details for Nptxr):

nervous system

Find genes that share phenotypes with NPTXR About GenesLikeMe

Animal Models:
MGI mouse knock-out Nptxr^tm1Mspn for NPTXR

genOway: Develop your customized and physiologically relevant rodent model for NPTXR

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In Situ Assay
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

NPTXR_HUMAN, O95502: Membrane; Single-pass type II membrane protein (Potential)

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
endoplasmic reticulum	2
extracellular	2
cytosol	1
nucleus	1
plasma membrane	1

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Gene Ontology (GO): 1 cellular component term: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0016021	integral component of membrane	IEA	--

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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for NPTXR About

See pathways by source

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SuperPath

Contained pathways About

Cellular Senescence

	Cellular Senescence	0.81			Oxidative Stress Induced Senescence	0.64
	Cellular responses to stress	0.81

Custom Pathway & Disease-focused RT² Profiler PCR Arrays for NPTXR
Interactions:

Search GeneGlobe Interaction Network for NPTXR

STRING Interaction Network Preview (showing 5 interactants - click image to see 15)

Selected Interacting proteins for NPTXR (O95502³ ENSP00000327545⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 17)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
NPTX2	P47972³, ENSP00000265634⁴	I2D: score=1 STRING: ENSP00000265634
NPTX1	Q15818³, ENSP00000307549⁴	I2D: score=1 STRING: ENSP00000307549
GBAS	O75323³	I2D: score=1
WIPI2	Q9Y4P8³	I2D: score=1
KLHL2	ENSP00000226725⁴	STRING: ENSP00000226725

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

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Browse compounds at ApexBio

Browse Tocris compounds for NPTXR

1 HMDB Compound for NPTXR About this table

Compound	Synonyms	CAS #	PubMed Ids
Calcium	Ca (see all 2)	7440-70-2	--

2 Novoseek inferred chemical compound relationships for NPTXR gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
cgmp	45.3	1	10446136 (1)
nadph	20.5	3	15089095 (2), 15547247 (1)

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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for NPTXR gene (2 alternative transcripts):

NM_014293.3 NM_058178.1

Unigene Cluster for NPTXR:

Neuronal pentraxin receptor

Hs.91622 [show with all ESTs]

Unigene Representative Sequence: NM_014293

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000333039(uc003awk.3)

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Additional mRNA sequence:

AF052163.1 AL161974.1 AL162057.1 BC043606.1

6 DOTS entries:

DT.100781229 DT.448345 DT.100781231 DT.120650937 DT.433700 DT.91909871

Selected AceView cDNA sequences (see all 212):

BQ230962 NM_014293 NM_058178 CD635634 AF052163 AI014314 BE048263 BU856929

AA372919 BM664678 BX090839 CB152312 BM722090 AA322700 D51955 BU632940

BC043606 T30973 CD635635 H41734 AW963649 T33852 R88792 AL118608

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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NPTXR expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: CTGTTTAAAA

About this image

NPTXR expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 2) fully expand


Brain (Nervous System)
Amygdala

Testis (Reproductive System)

NPTXR Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

NPTXR Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.91622

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In Situ
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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for NPTXR gene from Selected species (see all 11) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Nptxr^{1 , 5}	neuronal pentraxin receptor^{1, 5}	88.03(n)¹ 90.47(a)¹		15 (37.85 cM)⁵ 73340¹ NM_030689.4¹ NP_109614.2¹ 79786353⁵
chicken (Gallus gallus)	Aves	NPTXR⁶	neuronal pentraxin receptor	36(a)	1 ↔ 1	1(50627427-50649375)
lizard (Anolis carolinensis)	Reptilia	NPTXR⁶	neuronal pentraxin receptor	33(a)	1 ↔ 1	5(24307274-24385885)
zebrafish (Danio rerio)	Actinopterygii	nptxrb¹	neuronal pentraxin receptor b	55.26(n) 48.36(a)		100005257 NM_001044314.1 NP_001037779.1

ENSEMBL Gene Tree for NPTXR (if available)
TreeFam Gene Tree for NPTXR (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for NPTXR gene

NPTX2² APCS² CRP² PTX4² NPTX1² PTX3²

2 SIMAP similar genes for NPTXR using alignment to 1 protein entry: NPTXR_HUMAN:

NPTX2 NPTX1

Find genes that share paralogs with NPTXR About GenesLikeMe

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr 22 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs145231876^1,2	C	untested¹	39222748(+)	`GCTGAG/AGACCC`	2	/S	syn¹		1		NA	4546
rs116942161^1,2	C,F	--	22206071(+)	`GTCCAA/GGGTCA`	1	--	int¹		1		EA	120
rs12628473^1,2	C,H	--	22206303(+)	`TCATTA/GCAGAA`	1	--	int¹		2		CSA EA	122
rs12628497^1,2	C,A,H	--	22206306(+)	`TTACAG/AAATCT`	1	--	int¹		3		CSA WA EA	240
rs181231180^1,2		--	22206349(+)	`TCCTCC/TGAATC`	1	--	int¹		0	--	--	--	--
rs187094934^1,2		--	22206387(+)	`AGAGAA/TACCCC`	1	--	int¹		0	--	--	--	--
rs11913354^1,2	C,F,H	--	22206413(+)	`TCTGCC/TTTCGT`	1	--	int¹		1		WA	118
rs146109022^1,2		--	22206589(+)	`TAAAAA/GCAATC`	1	--	int¹		0	--	--	--	--
rs190629910^1,2	C	--	22206639(+)	`ATGAGA/GTCTTT`	1	--	int¹		0	--	--	--	--
rs183543611^1,2		--	22206657(+)	`AATACA/GGATTC`	1	--	int¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for NPTXR (39214456 - 39240017 bp)

Structural Variations
Database of Genomic Variants (DGV) 9 variations for NPTXR: About this table

Variant ID	Type	Subtype	PubMed ID
esv2724234	CNV	Deletion	23290073
esv2724233	CNV	Deletion	23290073
nsv915071	CNV	Loss	21882294
nsv915070	CNV	Loss	21882294
nsv915069	CNV	Loss	21882294
nsv471199	CNV	Loss	18288195
nsv915068	CNV	Loss	21882294
nsv915067	CNV	Loss	21882294
dgv769n67	CNV	Gain	20364138

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing NPTXR

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 609474 OMIM disorders: --

Find genes that share disorders with NPTXR About GenesLikeMe

Genetic Association Database (GAD): NPTXR
Human Genome Epidemiology (HuGE) Navigator: NPTXR (1 document)

Export disorders for NPTXR gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for NPTXR gene, integrated from 10 sources (see all 34):
(articles sorted by number of sources associating them with NPTXR)

Utopia: connect your pdf to the dynamic
world of online information

Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)^{1, 4} Rose J.E....Uhl G.R. (Mol. Med. 2010)
Regulation of neuronal type genes in congestive heart failure rats. (PubMed id 16497176)^{1, 3} Andersson K.B....Christensen G. (Acta Physiol (Oxf) 2006)
The DNA sequence of human chromosome 22. (PubMed id 10591208)^{1, 2} Dunham I.... Wright H. (Nature 1999)
Neuronal pentraxin receptor, a novel putative integral membrane pentraxin that interacts with neuronal pentraxin 1 and 2 and taipoxin-associated calcium-binding protein 49. (PubMed id 9261167)^{1, 9} Dodds D.C....Perin M.S. (J. Biol. Chem. 1997)
Neuronal pentraxin receptor in cerebrospinal fluid as a potential biomarker for neurodegenerative diseases. (PubMed id 19368810)^{1, 9} Yin G.N....Suk K. (Brain Res. 2009)
Specific sensitivity of small cell lung cancer cell lines to the snake venom toxin taipoxin. (PubMed id 16115696)^{1, 9} Poulsen T.T....Poulsen H.S. (Lung Cancer 2005)
Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)¹ Barbe L....Andersson-Svahn H. (amp 2008)
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)¹ Kimura K.... Sugano S. (Genome Res. 2006)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
Biochemical interactions of the neuronal pentraxins. Neuronal pentraxin (NP) receptor binds to taipoxin and taipoxin-associated calcium-binding protein 49 via NP1 and NP2. (PubMed id 10748068)¹ Kirkpatrick L.L.... Perin M.S. (J. Biol. Chem. 2000)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 23467	HGNC: 7954	AceView: NPTXR	Ensembl:ENSG00000221890	euGenes: HUgn23467
ECgene: NPTXR	H-InvDB: NPTXR

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for NPTXR	Pharmacogenomics, SNPs, Pathways

Intellectual Property for NPTXR gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for NPTXR gene:
Search GeneIP for patents involving NPTXR

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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Neuronal Pentraxin Receptor

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