APCS (amyloid P component, serum) - Rat Genome Database

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Gene: APCS (amyloid P component, serum) Homo sapiens
Analyze
Symbol: APCS
Name: amyloid P component, serum
RGD ID: 68444
HGNC Page HGNC
Description: Exhibits several functions, including complement component C1q complex binding activity; identical protein binding activity; and virion binding activity. Involved in several processes, including modulation by host of viral process; negative regulation of monocyte differentiation; and negative regulation of viral entry into host cell. Localizes to extracellular space. Implicated in amyloidosis.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: 9.5S alpha-1-glycoprotein; epididymis secretory sperm binding protein Li 92n; HEL-S-92n; MGC88159; pentaxin-related; pentraxin-2; pentraxin-related; PTX2; SAP; serum amyloid P-component
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC646430   MPTX1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1159,587,826 - 159,588,865 (+)EnsemblGRCh38hg38GRCh38
GRCh381159,587,826 - 159,588,865 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371159,557,616 - 159,558,655 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361157,824,240 - 157,825,285 (+)NCBINCBI36hg18NCBI36
Build 341156,370,688 - 156,371,733NCBI
Celera1132,627,015 - 132,628,060 (+)NCBI
Cytogenetic Map1q23.2NCBI
HuRef1130,914,686 - 130,915,731 (+)NCBIHuRef
CHM1_11160,953,113 - 160,954,158 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,7-dimethylxanthine  (ISO)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3-chloropropane-1,2-diol  (ISO)
3H-1,2-dithiole-3-thione  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
6-propyl-2-thiouracil  (ISO)
acetamide  (ISO)
acrylamide  (ISO)
Actein  (ISO)
aflatoxin B1  (EXP,ISO)
amiodarone  (ISO)
ammonium chloride  (ISO)
arsane  (EXP)
arsenic atom  (EXP)
benzbromarone  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (ISO)
cadmium atom  (EXP)
carbon nanotube  (ISO)
carrageenan  (ISO)
cefaloridine  (ISO)
choline  (ISO)
chromium trinitrate  (ISO)
ciprofibrate  (ISO)
clofibrate  (ISO)
clofibric acid  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
coumarin  (ISO)
cyclosporin A  (EXP)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
flutamide  (ISO)
folic acid  (ISO)
fumonisin B1  (ISO)
furan  (ISO)
gemcitabine  (EXP)
heparin  (EXP)
L-ethionine  (ISO)
L-methionine  (ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
lipopolysaccharide  (EXP,ISO)
mechlorethamine  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (ISO)
N-Nitrosopyrrolidine  (EXP)
nickel atom  (EXP)
O-methyleugenol  (EXP)
omeprazole  (ISO)
p-toluidine  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
resveratrol  (ISO)
sodium arsenite  (EXP)
sodium fluoride  (ISO)
tamoxifen  (EXP,ISO)
tetrachloromethane  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
triadimefon  (ISO)
Tributyltin oxide  (ISO)
troglitazone  (EXP)
tunicamycin  (ISO)
valsartan  (EXP)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Additional References at PubMed
PMID:81686   PMID:1477104   PMID:1602151   PMID:2987268   PMID:3029048   PMID:3172210   PMID:3211159   PMID:3759147   PMID:3915434   PMID:4055725   PMID:7592941   PMID:8114934  
PMID:8144569   PMID:8202534   PMID:8417122   PMID:8662978   PMID:8999915   PMID:9217261   PMID:10631319   PMID:10812074   PMID:10972085   PMID:11359830   PMID:11441067   PMID:11984001  
PMID:12100475   PMID:12126626   PMID:12432394   PMID:12477932   PMID:12528126   PMID:12767937   PMID:14500533   PMID:14519527   PMID:14607961   PMID:14718574   PMID:15031287   PMID:15174148  
PMID:15489334   PMID:15649951   PMID:15837583   PMID:16335952   PMID:16380821   PMID:16643876   PMID:16710414   PMID:16784490   PMID:17138933   PMID:17530641   PMID:17630380   PMID:17676666  
PMID:18174230   PMID:18624398   PMID:19011614   PMID:19052452   PMID:19056867   PMID:19372378   PMID:19948975   PMID:20189569   PMID:20237496   PMID:20300636   PMID:20551380   PMID:20930309  
PMID:20932823   PMID:21044893   PMID:21106539   PMID:21223953   PMID:21278351   PMID:21360619   PMID:21630459   PMID:21873635   PMID:21900206   PMID:21988832   PMID:22205573   PMID:22396542  
PMID:22493081   PMID:22516433   PMID:22528093   PMID:22867744   PMID:22939635   PMID:23376485   PMID:23385359   PMID:23390551   PMID:23423137   PMID:23527487   PMID:23533145   PMID:23544079  
PMID:23600950   PMID:23850452   PMID:23966633   PMID:23992930   PMID:24695531   PMID:24933153   PMID:25024390   PMID:25084341   PMID:26106150   PMID:26208400   PMID:26286643   PMID:27068509  
PMID:27428539   PMID:27559042   PMID:27754964   PMID:28098450   PMID:28434325   PMID:30097533   PMID:30862745   PMID:32296183   PMID:32814053  


Genomics

Comparative Map Data
APCS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1159,587,826 - 159,588,865 (+)EnsemblGRCh38hg38GRCh38
GRCh381159,587,826 - 159,588,865 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371159,557,616 - 159,558,655 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361157,824,240 - 157,825,285 (+)NCBINCBI36hg18NCBI36
Build 341156,370,688 - 156,371,733NCBI
Celera1132,627,015 - 132,628,060 (+)NCBI
Cytogenetic Map1q23.2NCBI
HuRef1130,914,686 - 130,915,731 (+)NCBIHuRef
CHM1_11160,953,113 - 160,954,158 (+)NCBICHM1_1
Apcs
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391172,721,528 - 172,722,621 (-)NCBIGRCm39mm39
GRCm39 Ensembl1172,721,528 - 172,722,608 (-)Ensembl
GRCm381172,893,961 - 172,895,054 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1172,893,961 - 172,895,041 (-)EnsemblGRCm38mm10GRCm38
MGSCv371174,824,092 - 174,825,185 (-)NCBIGRCm37mm9NCBIm37
MGSCv361174,730,637 - 174,731,718 (-)NCBImm8
Celera1175,741,973 - 175,743,066 (-)NCBICelera
Cytogenetic Map1H3NCBI
cM Map180.33NCBI
Apcs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21385,373,338 - 85,374,134 (-)NCBI
Rnor_6.0 Ensembl1391,426,479 - 91,427,575 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01391,426,621 - 91,427,417 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01395,938,118 - 95,938,914 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41389,112,845 - 89,113,641 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11389,301,610 - 89,302,610 (-)NCBI
Celera1384,980,649 - 84,981,445 (-)NCBICelera
Cytogenetic Map13q24NCBI
Apcs
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546811,388,192 - 11,390,314 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546811,388,154 - 11,389,259 (+)NCBIChiLan1.0ChiLan1.0
APCS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11138,734,046 - 138,735,093 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1138,734,046 - 138,735,093 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01134,937,472 - 134,938,512 (+)NCBIMhudiblu_PPA_v0panPan3
Apcs
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050585,767,140 - 5,768,100 (+)NCBI
SpeTri2.0NW_004936740979,007 - 987,312 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APCS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl490,898,686 - 90,901,875 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1490,900,585 - 90,901,854 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2498,901,214 - 98,901,460 (-)NCBISscrofa10.2Sscrofa10.2susScr3
APCS
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1204,360,955 - 4,363,810 (-)NCBI
ChlSab1.1 Ensembl204,358,654 - 4,362,095 (-)Ensembl
Vero_WHO_p1.0NW_0236660383,486,071 - 3,487,118 (-)NCBI
Apcs
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247941,689,619 - 1,690,700 (-)NCBI

Position Markers
RH11639  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371159,558,375 - 159,558,599UniSTSGRCh37
Build 361157,824,999 - 157,825,223RGDNCBI36
Celera1132,627,774 - 132,627,998RGD
Cytogenetic Map1q21-q23UniSTS
HuRef1130,915,445 - 130,915,669UniSTS
GeneMap99-GB4 RH Map1587.43UniSTS
NCBI RH Map11436.5UniSTS
D1S2412  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371159,558,328 - 159,558,449UniSTSGRCh37
Build 361157,824,952 - 157,825,073RGDNCBI36
Celera1132,627,727 - 132,627,848RGD
Cytogenetic Map1q21-q23UniSTS
HuRef1130,915,398 - 130,915,519UniSTS
GeneMap99-GB4 RH Map1590.02UniSTS
Whitehead-YAC Contig Map1 UniSTS
D1S3199  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371159,558,503 - 159,558,607UniSTSGRCh37
Build 361157,825,127 - 157,825,231RGDNCBI36
Celera1132,627,902 - 132,628,006RGD
Cytogenetic Map1q21-q23UniSTS
TNG Radiation Hybrid Map171949.0UniSTS
Stanford-G3 RH Map16127.0UniSTS
GeneMap99-GB4 RH Map1589.4UniSTS
NCBI RH Map11431.9UniSTS
GeneMap99-G3 RH Map16083.0UniSTS
RH93185  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371159,558,953 - 159,559,036UniSTSGRCh37
Build 361157,825,577 - 157,825,660RGDNCBI36
Celera1132,628,352 - 132,628,435RGD
Cytogenetic Map1q21-q23UniSTS
HuRef1130,916,023 - 130,916,106UniSTS
GeneMap99-GB4 RH Map1589.09UniSTS
APCS_8204  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371159,557,964 - 159,558,684UniSTSGRCh37
Build 361157,824,588 - 157,825,308RGDNCBI36
Celera1132,627,363 - 132,628,083RGD
HuRef1130,915,034 - 130,915,754UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:71
Interacting mature miRNAs:72
Transcripts:ENST00000255040
Prediction methods:Miranda, Rnahybrid, Targetscan
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.


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High 327 327 327
Medium 2 21 99 98 18 99 6 1 1 16 9 2 5 3
Low 87 209 92 22 173 16 87 55 65 61 86 105 7 43 56 1
Below cutoff 889 1002 520 74 503 3 1223 731 1118 100 554 500 72 401 819 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000255040   ⟹   ENSP00000255040
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1159,587,826 - 159,588,865 (+)Ensembl
RefSeq Acc Id: NM_001639   ⟹   NP_001630
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381159,587,826 - 159,588,865 (+)NCBI
GRCh371159,557,616 - 159,558,661 (+)ENTREZGENE
Build 361157,824,240 - 157,825,285 (+)NCBI Archive
HuRef1130,914,686 - 130,915,731 (+)ENTREZGENE
CHM1_11160,953,113 - 160,954,158 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001630   ⟸   NM_001639
- Peptide Label: precursor
- UniProtKB: P02743 (UniProtKB/Swiss-Prot),   V9HWP0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000255040   ⟸   ENST00000255040
Protein Domains
Pentraxin (PTX)

Promoters
RGD ID:6852610
Promoter ID:EP74117
Type:single initiation site
Name:HS_APCS
Description:Amyloid P component, serum.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Mammalian gene collection (MGC) full-length cDNA cloning
Position:
Human AssemblyChrPosition (strand)Source
Build 361157,824,240 - 157,824,300EPD
RGD ID:6857720
Promoter ID:EPDNEW_H2025
Type:multiple initiation site
Name:APCS_1
Description:amyloid P component, serum
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381159,587,826 - 159,587,886EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q23.2-24.1(chr1:159479887-166895086)x1 copy number loss See cases [RCV000051172] Chr1:159479887..166895086 [GRCh38]
Chr1:159449677..166864323 [GRCh37]
Chr1:157716301..165130947 [NCBI36]
Chr1:1q23.2-24.1
pathogenic
GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3 copy number gain See cases [RCV000051854] Chr1:157747246..176021247 [GRCh38]
Chr1:157717036..175990383 [GRCh37]
Chr1:155983660..174257006 [NCBI36]
Chr1:1q23.1-25.1
pathogenic
GRCh38/hg38 1q23.1-23.3(chr1:156664483-160727411)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051851]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051851]|See cases [RCV000051851] Chr1:156664483..160727411 [GRCh38]
Chr1:156634275..160697201 [GRCh37]
Chr1:154900899..158963825 [NCBI36]
Chr1:1q23.1-23.3
pathogenic
NM_001639.3(APCS):c.637G>A (p.Gly213Arg) single nucleotide variant Malignant melanoma [RCV000064245] Chr1:159588673 [GRCh38]
Chr1:159558463 [GRCh37]
Chr1:157825087 [NCBI36]
Chr1:1q23.2
not provided
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1q23.2(chr1:159475320-159621206)x1 copy number loss not provided [RCV000684665] Chr1:159475320..159621206 [GRCh37]
Chr1:1q23.2
likely benign
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1q23.1-24.2(chr1:157321299-167391423)x1 copy number loss not provided [RCV000848773] Chr1:157321299..167391423 [GRCh37]
Chr1:1q23.1-24.2
pathogenic
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:584 AgrOrtholog
COSMIC APCS COSMIC
Ensembl Genes ENSG00000132703 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000255040 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000255040 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000132703 GTEx
HGNC ID HGNC:584 ENTREZGENE
Human Proteome Map APCS Human Proteome Map
InterPro ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pentaxin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pentraxin-related UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:325 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 325 ENTREZGENE
OMIM 104770 OMIM
Pfam Pentaxin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA24877 PharmGKB
PRINTS PENTAXIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PTX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PTX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P02743 ENTREZGENE, UniProtKB/Swiss-Prot
  V9HWP0 ENTREZGENE, UniProtKB/TrEMBL