APOB (apolipoprotein B) - 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 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: APOB (apolipoprotein B) Canis lupus familiaris
Analyze
Symbol: APOB
Name: apolipoprotein B
RGD ID: 12435619
Description: ENCODES a protein that exhibits cholesterol transfer activity (inferred); heparin binding (inferred); lipase binding (inferred); INVOLVED IN artery morphogenesis (ortholog); cellular response to prostaglandin stimulus (ortholog); cellular response to tumor necrosis factor (ortholog); PARTICIPATES IN altered lipoprotein metabolic pathway; forkhead class A signaling pathway; lipoprotein metabolic pathway; ASSOCIATED WITH aortic valve stenosis (ortholog); arteriosclerosis (ortholog); autosomal recessive hypercholesterolemia (ortholog); FOUND IN extracellular space (ortholog); high-density lipoprotein particle (ortholog); low-density lipoprotein particle (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: apolipoprotein B (including Ag(x) antigen); apolipoprotein B-100
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11715,877,937 - 15,916,032 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1715,878,244 - 15,915,135 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1715,842,555 - 15,879,853 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01716,030,075 - 16,067,405 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1716,030,161 - 16,067,623 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11715,883,776 - 15,920,986 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01715,891,112 - 15,928,422 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01715,923,305 - 15,960,613 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
aortic valve stenosis  (ISO)
arteriosclerosis  (ISO)
autosomal recessive hypercholesterolemia  (ISO)
Behcet's disease  (ISO)
beta thalassemia  (ISO)
bile duct cancer  (ISO)
biliary tract cancer  (ISO)
cardiovascular system disease  (ISO)
celiac disease  (ISO)
cerebral infarction  (ISO)
common bile duct neoplasm  (ISO)
coronary artery disease  (ISO)
Coronary Disease  (ISO)
Coumarin Sensitivity  (ISO)
Death  (ISO)
diabetes mellitus  (ISO)
Diabetic Nephropathies  (ISO)
diabetic retinopathy  (ISO)
dilated cardiomyopathy 1B  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
Dyslipidemias  (ISO)
Endotoxemia  (ISO)
Experimental Diabetes Mellitus  (ISO)
familial combined hyperlipidemia  (ISO)
familial hypercholesterolemia  (ISO)
Familial Hypercholesterolemia due to Ligand-Defective Apolipoprotein B  (ISO)
familial hyperlipidemia  (ISO)
familial hypobetalipoproteinemia 1  (ISO)
familial hypobetalipoproteinemia 2  (ISO)
Familial Hypobetalipoproteinemia, Apolipoprotein B  (ISO)
familial isolated deficiency of vitamin E  (ISO)
gallbladder cancer  (ISO)
Hemorrhage  (ISO)
Hypercholesterolemia  (ISO)
Hypercholesterolemia, Autosomal Dominant, 3  (ISO)
Hyperlipoproteinemia Type II  (ISO)
Hypertriglyceridemia  (ISO)
hypobetalipoproteinemia  (ISO)
Isolated Systolic Hypertension  (ISO)
Marfanoid Mental Retardation Syndrome, Autosomal  (ISO)
Metabolic Syndrome  (ISO)
Myocardial Ischemia  (ISO)
nephrotic syndrome  (ISO)
obesity  (ISO)
ovarian cancer  (ISO)
sickle cell anemia  (ISO)
spastic ataxia  (ISO)
steatotic liver disease  (ISO)
Sudden Cardiac Death  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
warfarin resistance  (ISO)
warfarin sensitivity  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:8409768   PMID:10574922   PMID:30032202  


Genomics

Comparative Map Data
APOB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11715,877,937 - 15,916,032 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1715,878,244 - 15,915,135 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1715,842,555 - 15,879,853 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01716,030,075 - 16,067,405 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1716,030,161 - 16,067,623 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11715,883,776 - 15,920,986 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01715,891,112 - 15,928,422 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01715,923,305 - 15,960,613 (-)NCBIUU_Cfam_GSD_1.0
APOB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38221,001,429 - 21,044,073 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl221,001,429 - 21,044,073 (-)EnsemblGRCh38hg38GRCh38
GRCh37221,224,301 - 21,266,945 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36221,077,806 - 21,120,450 (-)NCBINCBI36Build 36hg18NCBI36
Build 34221,135,952 - 21,178,597NCBI
Celera221,063,779 - 21,106,429 (-)NCBICelera
Cytogenetic Map2p24.1NCBI
HuRef220,956,976 - 20,999,627 (-)NCBIHuRef
CHM1_1221,153,564 - 21,196,210 (-)NCBICHM1_1
T2T-CHM13v2.0221,034,648 - 21,077,293 (-)NCBIT2T-CHM13v2.0
Apob
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39128,027,629 - 8,066,839 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl128,027,648 - 8,066,835 (+)EnsemblGRCm39 Ensembl
GRCm38127,977,629 - 8,016,839 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl127,977,648 - 8,016,835 (+)EnsemblGRCm38mm10GRCm38
MGSCv37127,984,483 - 8,023,645 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36128,003,656 - 8,042,849 (+)NCBIMGSCv36mm8
Celera128,374,429 - 8,411,685 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map123.53NCBI
Apob
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8636,563,704 - 36,603,300 (+)NCBIGRCr8
mRatBN7.2630,844,386 - 30,883,983 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl630,844,368 - 30,892,497 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx631,136,522 - 31,176,112 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0631,452,442 - 31,492,039 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0630,926,947 - 30,966,539 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0633,176,826 - 33,216,381 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl633,176,778 - 33,224,997 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0642,956,372 - 42,995,922 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4631,508,060 - 31,548,083 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1631,546,139 - 31,550,758 (+)NCBI
Celera630,299,724 - 30,339,330 (+)NCBICelera
Cytogenetic Map6q14NCBI
Apob
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554693,436,450 - 3,478,424 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554693,437,422 - 3,478,408 (-)NCBIChiLan1.0ChiLan1.0
APOB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212105,485,757 - 105,528,305 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A105,489,857 - 105,532,277 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A20,986,464 - 21,029,004 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A21,100,349 - 21,142,545 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A21,100,356 - 21,145,129 (-)Ensemblpanpan1.1panPan2
Apob
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629260,290,128 - 60,327,775 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649310,509,118 - 10,549,144 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649310,509,118 - 10,549,144 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APOB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3117,250,096 - 117,316,200 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13117,250,096 - 117,316,200 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Pig Cytomap3q24-qterNCBI
APOB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11486,624,209 - 86,669,175 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1486,624,332 - 86,668,704 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604525,515,337 - 25,558,432 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Apob
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247383,580,033 - 3,620,192 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247383,579,747 - 3,622,508 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in APOB
369 total Variants

Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 5 5 23 22 16 6 6 6 6 33 22 12 14 10

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005630596 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038453019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038453020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038498324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038560882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038560883 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038624910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038624911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038690816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038690817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ399501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S65943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSCAFT00000006266   ⟹   ENSCAFP00000005806
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1715,878,244 - 15,915,135 (-)Ensembl
Ensembl Acc Id: ENSCAFT00845035808   ⟹   ENSCAFP00845028013
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1716,030,161 - 16,067,623 (-)Ensembl
RefSeq Acc Id: XM_038453019   ⟹   XP_038308947
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha1715,842,555 - 15,879,853 (-)NCBI
RefSeq Acc Id: XM_038453020   ⟹   XP_038308948
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha1715,845,475 - 15,879,853 (-)NCBI
RefSeq Acc Id: XM_038498324   ⟹   XP_038354252
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11715,883,776 - 15,920,986 (-)NCBI
RefSeq Acc Id: XM_038560882   ⟹   XP_038416810
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01715,923,305 - 15,960,613 (-)NCBI
RefSeq Acc Id: XM_038560883   ⟹   XP_038416811
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01715,926,224 - 15,960,613 (-)NCBI
RefSeq Acc Id: XM_038624910   ⟹   XP_038480838
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01715,891,112 - 15,928,422 (-)NCBI
RefSeq Acc Id: XM_038624911   ⟹   XP_038480839
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01715,894,031 - 15,928,422 (-)NCBI
RefSeq Acc Id: XM_038690816   ⟹   XP_038546744
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01716,030,075 - 16,067,405 (-)NCBI
RefSeq Acc Id: XM_038690817   ⟹   XP_038546745
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01716,032,994 - 16,067,405 (-)NCBI
Ensembl Acc Id: ENSCAFP00000005806   ⟸   ENSCAFT00000006266
RefSeq Acc Id: XP_038354252   ⟸   XM_038498324
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038480838   ⟸   XM_038624910
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038480839   ⟸   XM_038624911
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038546744   ⟸   XM_038690816
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LN65 (UniProtKB/TrEMBL),   A0A8I3S4D1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038546745   ⟸   XM_038690817
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LNZ9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038308947   ⟸   XM_038453019
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LN65 (UniProtKB/TrEMBL),   A0A8P0S9H4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038308948   ⟸   XM_038453020
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LNZ9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038416810   ⟸   XM_038560882
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LN65 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038416811   ⟸   XM_038560883
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LNZ9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845028013   ⟸   ENSCAFT00845035808
Protein Domains
Vitellogenin


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000003887 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030016297 UniProtKB/TrEMBL
  ENSCAFG00845020315 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000006266.4 UniProtKB/TrEMBL
  ENSCAFT00030030156.1 UniProtKB/TrEMBL
  ENSCAFT00845035808 ENTREZGENE
  ENSCAFT00845035808.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.20 UniProtKB/TrEMBL
  Lipovitellin-phosvitin complex, chain A, domain 4 UniProtKB/TrEMBL
InterPro ApoB100_C UniProtKB/TrEMBL
  Apolipoprotein_B UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Lipid_transp_b-sht_shell UniProtKB/TrEMBL
  Lipid_transpt_N UniProtKB/TrEMBL
  Lipid_transpt_open_b-sht UniProtKB/TrEMBL
  Lipovitellin_superhlx_dom UniProtKB/TrEMBL
  Vitellinogen_b-sht_N UniProtKB/TrEMBL
  Vitellinogen_open_b-sht UniProtKB/TrEMBL
NCBI Gene APOB ENTREZGENE
PANTHER APOLIPOPROTEIN B UniProtKB/TrEMBL
  APOLIPOPROTEIN B-100 UniProtKB/TrEMBL
Pfam ApoB100_C UniProtKB/TrEMBL
  DUF1081 UniProtKB/TrEMBL
  DUF1943 UniProtKB/TrEMBL
  Vitellogenin_N UniProtKB/TrEMBL
PROSITE VITELLOGENIN UniProtKB/TrEMBL
SMART DUF1943 UniProtKB/TrEMBL
  LPD_N UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
  SSF48431 UniProtKB/TrEMBL
UniProt A0A8C0LN65 ENTREZGENE
  A0A8C0LNZ9 ENTREZGENE
  A0A8C0NG66_CANLF UniProtKB/TrEMBL
  A0A8I3S4D1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0S9H4 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:37994 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-09-12 APOB  apolipoprotein B    apolipoprotein B-100  Symbol and/or name change 5135510 APPROVED