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Set Analyses:

VarElect

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APCS Gene

protein-coding GIFtS: 64
GCID: GC01P159557

Amyloid P Component, Serum

Alzheimer's & Parkinson's Diseases Congress

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at

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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
Amyloid P Component, Serum¹ ²		PTX2² ³
9.5S Alpha-1-Glycoprotein¹ ² ³		HEL-S-92n²
SAP² ³ ⁵		Epididymis Secretory Sperm Binding Protein Li 92n²
pentaxin-related¹ ²		Serum Amyloid P-Component²

External Ids:	HGNC: 584¹	Entrez Gene: 325²	Ensembl: ENSG00000132703⁷	OMIM: 104770⁵	UniProtKB: P02743³

Export aliases for APCS gene to outside databases

Previous GC identifers: GC01P157349 GC01P155289 GC01P156335 GC01P156774 GC01P156370 GC01P157824 GC01P130914

(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 APCS Gene:

The protein encoded by this gene is a glycoprotein, belonging to the pentraxin family of proteins, which has a

characteristic pentameric organization. These family members have considerable sequence homology which is thought

to be the result of gene duplication. The binding of the encoded protein to proteins in the pathological amyloid

cross-beta fold suggests its possible role as a chaperone. This protein is also thought to control the

degradation of chromatin. It has been demonstrated that this protein binds to apoptotic cells at an early stage,

which raises the possibility that it is involved in dealing with apoptotic cells in vivo. (provided by RefSeq,

Sep 2008)

GeneCards Summary for APCS Gene:

APCS (amyloid P component, serum) is a protein-coding gene. Diseases associated with APCS include amyloidosis, secondary, and candida glabrata. GO annotations related to this gene include unfolded protein binding. An important paralog of this gene is NPTX2.

UniProtKB/Swiss-Prot: SAMP_HUMAN, P02743

Function: Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating

cells. May also function as a calcium-dependent lectin

Gene Wiki entry for APCS (Serum amyloid P component) 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:

NC_000001.11 NC_018912.2 NT_004487.20

Regulatory elements:

Regulatory transcription factor binding sites in the APCS gene promoter:
Nkx3-1 Nkx3-1 v4 Nkx3-1 v1 STAT5A NF-E2 p45 Nkx3-1 v2 Zic1 STAT3 Nkx3-1 v3 NF-E2
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: APCS promoter sequence

Search Chromatin IP Primers for APCS

Epigenetics:

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

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

Entrez Gene cytogenetic band: 1q21-q23 Ensembl cytogenetic band: 1q23.2 HGNC cytogenetic band: 1q21-q23

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

GeneLoc information about chromosome 1 GeneLoc Exon Structure

GeneLoc location for GC01P159557: view genomic region (about GC identifiers)

Start:	159,557,615 bp from pter	End:	159,558,661 bp from pter
Size:	1,047 bases	Orientation:	plus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SAMP_HUMAN, P02743 (See protein sequence)

Recommended Name: Serum amyloid P-component precursor

Size: 223 amino acids; 25387 Da

Cofactor: Binds 2 calcium ions per subunit

Subunit: Homopentamer. Pentaxin (or pentraxin) have a discoid arrangement of 5 non-covalently bound subunits

Mass spectrometry: Mass=25462.5; Mass_error=1.1; Method=Electrospray; Range=20-223; Source=PubMed:8202534;

Mass spectrometry: Mass=25463; Mass_error=3; Method=MALDI; Range=20-223; Source=PubMed:15174148;

Mass spectrometry: Mass=1285.78; Method=MALDI; Range=213-223; Source=PubMed:15174148;

Mass spectrometry: Mass=1186.71; Method=MALDI; Range=213-222; Source=PubMed:15174148;

Selected PDB 3D structures from and Proteopedia for APCS (see all 13):

1GYK (3D)

1LGN (3D)

1SAC (3D)

2A3W (3D)

2A3X (3D)

2A3Y (3D)

Explore the universe of human proteins at neXtProt for APCS: NX_P02743

Explore proteomics data for APCS at MOPED

Post-translational modifications:

N-glycosylated with a complex biantennary oligosaccharide chain with a sialic acid at the end (disialo-SAP).

Monosialo-SAP as well as asioalo-SAP are also detected (PubMed:15174148)¹

Glycosylation² at Asn51

Modification sites at PhosphoSitePlus

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

REFSEQ proteins: NP_001630.1

ENSEMBL proteins:

ENSP00000255040

Reactome Protein details: P02743

APCS Human Recombinant Protein Products:

	Browse Purified and Recombinant Proteins at EMD Millipore
	R&D Systems Recombinant & Natural Proteins for APCS (Pentraxin 2/SAP)
	Browse recombinant and purified proteins available from Enzo Life Sciences
	OriGene Purified Proteins for APCS OriGene Protein Over-expression Lysate for APCS OriGene MassSpec for APCS OriGene Custom Protein Services for APCS
	GenScript Custom Purified and Recombinant Proteins Services for APCS
	Novus Biologicals APCS Proteins Novus Biologicals APCS Lysate
	Sino Biological Recombinant Protein for APCS Sino Biological Cell Lysate for APCS
	ProSpec Recombinant Protein for APCS
	Browse Proteins at Cloud-Clone Corp.

APCS Antibody Products:

	EMD Millipore Mono- and Polyclonal Antibodies for the study of APCS
	R&D Systems Antibodies for APCS (Pentraxin 2/SAP)
	OriGene Antibodies for APCS OriGene Custom Antibody Services for APCS
	Novus Biologicals APCS Antibodies
	Abcam antibodies for APCS
	Browse Antibodies at Cloud-Clone Corp.
	ThermoFisher Antibodies for APCS
	LSBio Antibodies in human, mouse, rat for APCS

APCS Assay Products:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Assay Services for APCS
	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for APCS
	Browse Enzo Life Sciences for kits & assays
	Browse ELISAs at Cloud-Clone Corp. Browse CLIAs at Cloud-Clone Corp.

(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 P02743

ProtoNet protein and cluster: P02743

1 Blocks protein domain: IPB001759 Pentaxin

UniProtKB/Swiss-Prot: SAMP_HUMAN, P02743

Similarity: Belongs to the pentaxin family

Similarity: Contains 1 pentaxin domain

APCS for domains About GeneDecksing

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: SAMP_HUMAN, P02743

Function: Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating

cells. May also function as a calcium-dependent lectin

Genatlas biochemistry entry for APCS:

amyloid P component,serum,pentaxin (pentraxin) family

Gene Ontology (GO): 2 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0046872	metal ion binding	IEA	--
GO:0051082	unfolded protein binding	TAS	10812074

APCS for ontologies About GeneDecksing

Phenotypes:
1 GenomeRNAi human phenotype for APCS:

Decreased viability of wild-ty

5 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Apcs):

hematopoietic system

immune system

mortality/aging

other

renal/urinary system

APCS for phenotypes About GeneDecksing

Animal Models:
MGI mouse knock-outs for APCS: Apcs^tm1Mpe Apcs^tm1Smae

inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for APCS

inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for APCS

genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for APCS

genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for APCS

miRNA Products:		Block miRNA regulation of human, mouse, rat APCS using miScript Target Protectors
		Search for qRT-PCR Assays for microRNAs that regulate APCS
		SwitchGear 3'UTR luciferase reporter plasmid: APCS 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for APCS
		Predesigned siRNA for gene silencing in human, mouse, rat APCS

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for APCS

Clone Products:		OriGene clones in human, mouse for APCS (see all 6) OriGene ORF clones in mouse, rat for APCS OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: APCS (NM_001639)
		Sino Biological Human cDNA Clone for APCS
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for APCS
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat APCS

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for APCS
		Browse ESI BIO Cell Lines and PureStem Progenitors for APCS

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for APCS

(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

SAMP_HUMAN, P02743: Secreted

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
extracellular	5
nucleus	2
cytoskeleton	1
mitochondrion	1
peroxisome	1

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Gene Ontology (GO): Selected cellular component terms (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	TAS	--
GO:0005615	extracellular space	IDA	--
GO:0031012	colocalizes with extracellular matrix	IDA	--
GO:0043234	protein complex	IEA	--
GO:0070062	extracellular vesicular exosome	IDA	19056867

APCS for ontologies About GeneDecksing

(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 APCS About

See pathways by source

SuperPath

Contained pathways About

RNA Polymerase I Promoter Opening

Amyloids

0.68

Selected targets of C EBPbeta

Selected targets of C EBPbeta

Disease

Disease

Pathways by source See SuperPaths
Show all pathways

1 Reactome Pathway for APCS

Amyloids

APCS for pathways About GeneDecksing

Pathway & Disease-focused RT² Profiler PCR Arrays including APCS:

Innate & Adaptive Immune Responses in human mouse rat

Inflammatory Response & Autoimmunity 384HT in human mouse rat

Antibacterial Response in human mouse rat

Interactions:

GeneGlobe Interaction Network for APCS

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for APCS (P02743^{2, 3} ENSP00000255040⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 41)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
GOT2	P00505²^,³, ENSP00000245206⁴	MINT-8249003 I2D: score=2 STRING: ENSP00000245206
HES1	Q14469²^,³, ENSP00000232424⁴	MINT-8249014 I2D: score=2 STRING: ENSP00000232424
C4BPA	P04003³, ENSP00000356037⁴	I2D: score=2 STRING: ENSP00000356037
CALU	O43852³, ENSP00000249364⁴	I2D: score=2 STRING: ENSP00000249364
FCGR3A	P08637³, ENSP00000356946⁴	I2D: score=2 STRING: ENSP00000356946

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Gene Ontology (GO): 4 biological process terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006457	protein folding	TAS	10812074
GO:0006461	protein complex assembly	--	--
GO:0006953	acute-phase response	TAS	2987268
GO:0051131	chaperone-mediated protein complex assembly	TAS	10972085

APCS for ontologies About GeneDecksing

(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

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for APCS (SAMP)

1 HMDB Compound for APCS About this table

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

3 DrugBank Compounds for APCS About this table

Compound	Synonyms	CAS #	Type	Actions	PubMed Ids
Methyl 4,6-O-[(1r)-1-Carboxyethylidene]-Beta-D-Galactopyranoside	--	--	target	--	17139284 17016423
BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE	--	--	target	--	10592235
BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE	--	--	target	--	10592235

8 Novoseek inferred chemical compound relationships for APCS gene About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
saquinavir	67.7	1	12182226 (1)
indinavir	64.1	2	12182226 (1), 10532286 (1)
ganglioside	29.7	1	12733985 (1)
phosphatidylethanolamine	26	5	11441067 (3), 8999915 (1)
ceramide	25.2	1	12733985 (1)
phospholipid	23.1	2	11441067 (1), 12609906 (1)
anti-fungal	19.7	1	10450995 (1)
lipid	0	1	15530444 (1)

APCS for compounds About GeneDecksing

(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for APCS gene:

NM_001639.3

Unigene Cluster for APCS:

Amyloid P component, serum

Hs.507080 [show with all ESTs]

Unigene Representative Sequence: BG533315

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

ENST00000255040(uc001ftv.3)

miRNA Products:		Block miRNA regulation of human, mouse, rat APCS using miScript Target Protectors
		Search for qRT-PCR Assays for microRNAs that regulate APCS
		SwitchGear 3'UTR luciferase reporter plasmid: APCS 3' UTR sequence

Inhib. RNA Products:		OriGene RNAi products in human, mouse, rat for APCS
		Predesigned siRNA for gene silencing in human, mouse, rat APCS

Clone Products:		OriGene clones in human, mouse for APCS (see all 6) OriGene ORF clones in mouse, rat for APCS OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: APCS (NM_001639)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for APCS
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat APCS

Primer Products:		OriGene qPCR primer pairs and template standards for APCS OriGene qSTAR qPCR primer pairs in human, mouse for APCS
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat APCS
		QuantiTect SYBR Green Assays in human, mouse, rat APCS
		QuantiFast Probe-based Assays in human, mouse, rat APCS

Additional mRNA sequence:

BC007039.1 BC007058.1 BC070178.1 BT006750.1 CR450313.1 M10944.1 X04608.1

3 DOTS entries:

DT.413275 DT.91827599 DT.92447980

Selected AceView cDNA sequences (see all 177):

AV659282 C20929 CK904372 AV659408 AV653918 BG568058 AV658456 BG533525

BG618846 CK904371 CB162114 BG567413 BG617439 BG533315 BG569529 BG562390

BG562396 BG569117 BG617984 BG563941 BG565555 BG567133 BG618324 BG545320

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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APCS expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: TGGGACTCTG

About this image

APCS expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 3) fully expand


Liver (Hepatobiliary System)
Hepatocytes Liver Lobule

Lung (Respiratory System)

Gall Bladder (Hepatobiliary System)

APCS Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

APCS Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.507080

UniProtKB/Swiss-Prot: SAMP_HUMAN, P02743

Tissue specificity: Found in serum and urine

Pathway & Disease-focused RT² Profiler PCR Arrays including APCS:

Innate & Adaptive Immune Responses in human mouse rat

Inflammatory Response & Autoimmunity 384HT in human mouse rat

Antibacterial Response in human mouse rat

Primer Products:		OriGene qPCR primer pairs and template standards for APCS OriGene qSTAR qPCR primer pairs in human, mouse for APCS
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat APCS
		QuantiTect SYBR Green Assays in human, mouse, rat APCS
		QuantiFast Probe-based Assays in human, mouse, rat APCS

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for APCS

(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 APCS gene from Selected species (see all 9) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Apcs^{1 , 5}	serum amyloid P-component^{1, 5}	74.02(n)¹ 69.37(a)¹		1 (80.33 cM)⁵ 20219¹ NM_011318.2¹ NP_035448.2¹ 172893962⁵
chicken (Gallus gallus)	Aves	CRP⁶	Gallus gallus C-reactive protein, pentraxin-relate...	45(a)	1 → many	25(1674627-1675765)
lizard (Anolis carolinensis)	Reptilia	-- -- (see all 5)	Uncharacterized protein (see all 5)	43(a) 42(a) (see all 5)	many ↔ many many ↔ many (see all 5)	GL343640.1(60469-66673) GL343640.1(49346-56006)
zebrafish (Danio rerio)	Actinopterygii	crp2⁶ crp3⁶ (see all 7)	C-reactive protein 3 (see all 7)	35(a) 32(a) (see all 7)	many ↔ many many ↔ many (see all 7)	24(39585485-39588803) ENSDARG00000056462 24(39591921-39600319) ENSDARG00000042613

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

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

NPTX2² CRP² PTX4² NPTX1² NPTXR² PTX3²

2 SIMAP similar genes for APCS using alignment to 1 protein entry: SAMP_HUMAN:

CRP MPTX1

APCS for paralogs About GeneDecksing

2 Pseudogenes.org Pseudogenes for APCS
PGOHUM00000245032 PGOHUM00000245035

(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 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
VAR_035814⁴		A breast cancer sample⁴	--	see VAR_035814	2	G S	mis⁴		0	--	--	--	--
rs189362597^1,2		--	159555892(+)	`AAGTAC/TGAAAG`	1	--	us2k¹		0	--	--	--	--
rs180868488^1,2		--	159555915(+)	`GTATAG/TTTGGG`	1	--	us2k¹		0	--	--	--	--
rs2808646^1,2	C,F,A	--	159555924(+)	`GGATAT/ATAGAA`	1	--	us2k¹		1		WA	118
rs35311861^1,2	C	--	159556051(+)	`ACTATA/GACCAT`	1	--	us2k¹		2		NA EA	122
rs184923858^1,2		--	159556080(+)	`ATTAAC/TGTGGA`	1	--	us2k¹		0	--	--	--	--
rs147725236^1,2		--	159556140(+)	`CAAGAC/GAGTAT`	1	--	us2k¹		0	--	--	--	--
rs189767386^1,2		--	159556333(+)	`ATAATC/GCCAAC`	1	--	us2k¹		0	--	--	--	--
rs142027932^1,2		--	159556341(+)	`AACTTC/TATCAC`	1	--	us2k¹		0	--	--	--	--
rs10494327^1,2	F	--	159556451(+)	`GAAGGA/TTACTT`	1	--	us2k¹		6		NS NA	226

HapMap Linkage Disequilibrium report for APCS (159557615 - 159558661 bp)

Structural Variations
Database of Genomic Variants (DGV) variations for APCS: --

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing APCS

DNA2.0 Custom Variant and Variant Library Synthesis for APCS

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 104770 OMIM disorders: --

UniProtKB/Swiss-Prot: SAMP_HUMAN, P02743

Note=SAP is a precursor of amyloid component P which is found in basement membrane and associated with

amyloid deposits

Selected diseases for APCS (see all 30):
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amyloidosis, secondary candida glabrata oral candidiasis carpal tunnel syndrome

candidiasis endocarditis vaginitis burns

polyneuropathy amyloidosis pulmonary fibrosis systemic lupus erythematosus

dementia influenza breast and colorectal cancer lupus erythematosus

parkinson's disease atherosclerosis hepatitis b alzheimer's disease

3 diseases from the University of Copenhagen DISEASES database for APCS:

Amyloidosis Polyneuropathy Alzheimer's disease

APCS for disorders About GeneDecksing

Congresses - knowledge worth sharing:
The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014
Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

6 Novoseek inferred disease relationships for APCS gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
candidiasis	69.4	3	11556759 (1), 12437091 (1), 17472610 (1)
oropharyngeal	51.2	1	17472610 (1)
response acute phase	42.7	1	16380821 (1)
immunodeficiency	19.8	4	12182226 (1), 10532286 (1), 15770446 (1), 15094164 (1)
inflammation	19.3	1	17138933 (1)
aids	16.6	1	10770752 (1)

Genetic Association Database (GAD): APCS
Human Genome Epidemiology (HuGE) Navigator: APCS (11 documents)

Export disorders for APCS 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 APCS gene, integrated from 10 sources (see all 137):
(articles sorted by number of sources associating them with APCS)

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

Human serum amyloid P component. cDNA isolation, complete sequence of pre-serum amyloid P component, and localization of the gene to chromosome 1. (PubMed id 2987268)^{1, 2, 3} Mantzouranis E.C.... Colten H.R. (J. Biol. Chem. 1985)
Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy: complexity in a single-gene disease. (PubMed id 15649951)^{1, 4, 9} Soares M.L....Buxbaum J.N. (Hum. Mol. Genet. 2005)
Integrative predictive model of coronary artery calcification in atherosclerosis. (PubMed id 19948975)^{1, 4} McGeachie M....Ramoni M.F. (Circulation 2009)
Association of polymorphisms in complement component C3 gene with susceptibility to systemic lupus erythematosus. (PubMed id 18174230)^{1, 4} Miyagawa H....Horiuchi T. (Rheumatology (Oxford) 2008)
The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)^{1, 2} Gregory S.G.... Bentley D.R. (Nature 2006)
Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)^{1, 2} Liu T.... Smith R.D. (J. Proteome Res. 2005)
Proteomic characterization of novel serum amyloid P component variants from human plasma and urine. (PubMed id 15174148)^{1, 2} Kiernan U.A.... Nelson R.W. (Proteomics 2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S.... Malek J. (Genome Res. 2004)
Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP. (PubMed id 9217261)^{1, 2} Hohenester E.... Wood S.P. (J. Mol. Biol. 1997)
Human serum amyloid P component is an invariant constituent of amyloid deposits and has a uniquely homogeneous glycostructure. (PubMed id 8202534)^{1, 2} Pepys M.B.... Dwek R.A. (Proc. Natl. Acad. Sci. U.S.A. 1994)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
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: 325	HGNC: 584	AceView: APCS	Ensembl:ENSG00000132703	euGenes: HUgn325
ECgene: APCS	H-InvDB: APCS

(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 APCS	Pharmacogenomics, SNPs, Pathways
Wikipedia	http://en.wikipedia.org/wiki/Serum_Amyloid_P_Component

Intellectual Property for APCS 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 APCS gene:
Search GeneIP for patents involving APCS

GeneCards and IP:
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(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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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