APOC4 (apolipoprotein C4) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: APOC4 (apolipoprotein C4) Homo sapiens
Analyze
Symbol: APOC4
Name: apolipoprotein C4
RGD ID: 736043
HGNC Page HGNC
Description: Predicted to have lipid transporter activity. Involved in positive regulation of sequestering of triglyceride and triglyceride homeostasis. Localizes to high-density lipoprotein particle and very-low-density lipoprotein particle.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: APO-CIV; APOC-IV; apolipoprotein C-IV
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1944,942,237 - 44,945,496 (+)EnsemblGRCh38hg38GRCh38
GRCh381944,942,237 - 44,945,496 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371945,445,494 - 45,448,753 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361950,137,335 - 50,140,591 (+)NCBINCBI36hg18NCBI36
Build 341950,137,334 - 50,140,591NCBI
Celera1942,249,817 - 42,253,073 (+)NCBI
Cytogenetic Map19q13.32NCBI
HuRef1941,875,522 - 41,879,312 (+)NCBIHuRef
CHM1_11945,448,327 - 45,451,585 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. GOA_HUMAN data from the GO Consortium
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8530039   PMID:8827523   PMID:8910501   PMID:10996355   PMID:11752456   PMID:12032151   PMID:12477932   PMID:12700345   PMID:15489334   PMID:16335952   PMID:16344560   PMID:16763159  
PMID:17154273   PMID:18193043   PMID:18193044   PMID:18802019   PMID:18809223   PMID:19060906   PMID:19197348   PMID:19336475   PMID:19913121   PMID:20331378   PMID:20430392   PMID:20498921  
PMID:20571754   PMID:20602615   PMID:20628086   PMID:20714348   PMID:20855565   PMID:20864672   PMID:20972250   PMID:21103663   PMID:21873635   PMID:21943158   PMID:25378659   PMID:26129832  
PMID:32296183  


Genomics

Candidate Gene Status
APOC4 is a candidate Gene for QTL BW139_H
Comparative Map Data
APOC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1944,942,237 - 44,945,496 (+)EnsemblGRCh38hg38GRCh38
GRCh381944,942,237 - 44,945,496 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371945,445,494 - 45,448,753 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361950,137,335 - 50,140,591 (+)NCBINCBI36hg18NCBI36
Build 341950,137,334 - 50,140,591NCBI
Celera1942,249,817 - 42,253,073 (+)NCBI
Cytogenetic Map19q13.32NCBI
HuRef1941,875,522 - 41,879,312 (+)NCBIHuRef
CHM1_11945,448,327 - 45,451,585 (+)NCBICHM1_1
Apoc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39719,412,009 - 19,415,385 (-)NCBIGRCm39mm39
GRCm39 Ensembl719,412,008 - 19,415,404 (-)Ensembl
GRCm38719,678,084 - 19,681,460 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl719,678,083 - 19,681,479 (-)EnsemblGRCm38mm10GRCm38
MGSCv37720,263,443 - 20,266,765 (-)NCBIGRCm37mm9NCBIm37
MGSCv36718,836,616 - 18,839,938 (-)NCBImm8
Celera717,084,177 - 17,087,500 (-)NCBICelera
Cytogenetic Map7A3NCBI
cM Map79.94NCBI
Apoc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2179,335,745 - 79,339,942 (-)NCBI
Rnor_6.0 Ensembl180,595,326 - 80,599,572 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0180,595,339 - 80,599,525 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0181,860,928 - 81,865,003 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4178,985,350 - 78,989,564 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1179,063,617 - 79,067,655 (+)NCBI
Celera173,795,049 - 73,799,140 (-)NCBICelera
Cytogenetic Map1q21NCBI
Apoc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555552,018,327 - 2,018,828 (+)NCBIChiLan1.0ChiLan1.0
APOC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11950,495,239 - 50,498,194 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01941,889,099 - 41,892,546 (+)NCBIMhudiblu_PPA_v0panPan3
APOC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1110,507,489 - 110,509,647 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11110,507,449 - 110,509,684 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Apoc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367061,528,187 - 1,530,028 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APOC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1651,400,909 - 51,403,719 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2647,282,628 - 47,285,470 (+)NCBISscrofa10.2Sscrofa10.2susScr3
APOC4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1638,391,454 - 38,406,692 (+)NCBI
ChlSab1.1 Ensembl638,398,471 - 38,406,697 (+)Ensembl

Position Markers
RH46551  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371945,448,503 - 45,448,695UniSTSGRCh37
Build 361950,140,343 - 50,140,535RGDNCBI36
Celera1942,252,825 - 42,253,017RGD
Cytogenetic Map19q13.2UniSTS
HuRef1941,879,062 - 41,879,254UniSTS
GeneMap99-GB4 RH Map19250.55UniSTS
RH18398  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371945,448,563 - 45,448,746UniSTSGRCh37
Build 361950,140,403 - 50,140,586RGDNCBI36
Celera1942,252,885 - 42,253,068RGD
Cytogenetic Map19qUniSTS
Cytogenetic Map19q13.2UniSTS
HuRef1941,879,122 - 41,879,305UniSTS
GeneMap99-GB4 RH Map19250.75UniSTS
NCBI RH Map19484.8UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:571
Count of miRNA genes:453
Interacting mature miRNAs:489
Transcripts:ENST00000591600, ENST00000592954
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.


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
High
Medium 7 227 226 8 226 2
Low 33 162 301 19 222 18 107 12 480 1 124 266 1 43 73
Below cutoff 1032 1041 687 231 547 129 1996 854 2295 61 721 666 103 657 1307

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000591600   ⟹   ENSP00000466444
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1944,942,274 - 44,945,016 (+)Ensembl
RefSeq Acc Id: ENST00000592954   ⟹   ENSP00000468236
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1944,942,237 - 44,945,496 (+)Ensembl
RefSeq Acc Id: NM_001646   ⟹   NP_001637
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381944,942,237 - 44,945,496 (+)NCBI
GRCh371945,445,495 - 45,448,753 (+)ENTREZGENE
Build 361950,137,335 - 50,140,591 (+)NCBI Archive
HuRef1941,875,522 - 41,879,312 (+)ENTREZGENE
CHM1_11945,448,327 - 45,451,585 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001637   ⟸   NM_001646
- Peptide Label: precursor
- UniProtKB: P55056 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000466444   ⟸   ENST00000591600
RefSeq Acc Id: ENSP00000468236   ⟸   ENST00000592954

Promoters
RGD ID:7240363
Promoter ID:EPDNEW_H25928
Type:initiation region
Name:APOC4_1
Description:apolipoprotein C4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381944,942,274 - 44,942,334EPDNEW
RGD ID:6814628
Promoter ID:HG_XEF:4133
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:NM_001082365,   NM_007385
Position:
Human AssemblyChrPosition (strand)Source
Build 361950,138,846 - 50,139,346 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh37/hg19 19q13.2-13.32(chr19:43013365-47241534)x1 copy number loss See cases [RCV000240182] Chr19:43013365..47241534 [GRCh37]
Chr19:19q13.2-13.32
pathogenic
GRCh37/hg19 19q13.32(chr19:45284576-45978239)x3 copy number gain See cases [RCV000239782] Chr19:45284576..45978239 [GRCh37]
Chr19:19q13.32
uncertain significance
GRCh37/hg19 19q13.31-13.32(chr19:44300416-45639540)x1 copy number loss See cases [RCV000512107] Chr19:44300416..45639540 [GRCh37]
Chr19:19q13.31-13.32
uncertain significance
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888) copy number gain See cases [RCV000512296] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888)x3 copy number gain See cases [RCV000511289] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic|uncertain significance
GRCh37/hg19 19q13.32(chr19:45338895-45618902)x3 copy number gain not provided [RCV000752710] Chr19:45338895..45618902 [GRCh37]
Chr19:19q13.32
benign
GRCh37/hg19 19p13.3-q13.43(chr19:68029-59110290)x3 copy number gain not provided [RCV000752439] Chr19:68029..59110290 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-59097160)x3 copy number gain not provided [RCV000752444] Chr19:260912..59097160 [GRCh37]
Chr19:19p13.3-q13.43
pathogenic
GRCh37/hg19 19q13.31-13.42(chr19:44738088-53621561)x3 copy number gain not provided [RCV001007050] Chr19:44738088..53621561 [GRCh37]
Chr19:19q13.31-13.42
pathogenic
GRCh37/hg19 19q11-13.33(chr19:28271106-49213832)x3 copy number gain not provided [RCV000845733] Chr19:28271106..49213832 [GRCh37]
Chr19:19q11-13.33
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:611 AgrOrtholog
COSMIC APOC4 COSMIC
Ensembl Genes ENSG00000267467 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000466444 UniProtKB/TrEMBL
  ENSP00000468236 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000591600 UniProtKB/TrEMBL
  ENST00000592954 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000267467 GTEx
HGNC ID HGNC:611 ENTREZGENE
Human Proteome Map APOC4 Human Proteome Map
InterPro APOC4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:346 UniProtKB/Swiss-Prot
NCBI Gene 346 ENTREZGENE
OMIM 600745 OMIM
PANTHER PTHR32288 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam APOC4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA54 PharmGKB
UniProt A5YAK2_HUMAN UniProtKB/TrEMBL
  APOC4_HUMAN UniProtKB/Swiss-Prot
  K7EMC3_HUMAN UniProtKB/TrEMBL
  P55056 ENTREZGENE
UniProt Secondary B3KWY6 UniProtKB/Swiss-Prot
  Q53YY8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-03 APOC4  apolipoprotein C4    apolipoprotein C-IV  Symbol and/or name change 5135510 APPROVED