Apof (apolipoprotein F) - Rat Genome Database

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Gene: Apof (apolipoprotein F) Rattus norvegicus
Analyze
Symbol: Apof
Name: apolipoprotein F
RGD ID: 1560713
Description: Predicted to be involved in cholesterol metabolic process. Predicted to act upstream of or within cholesterol efflux and triglyceride metabolic process. Predicted to be part of high-density lipoprotein particle and low-density lipoprotein particle. Predicted to be active in extracellular space. Orthologous to human APOF (apolipoprotein F); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: VALIDATED
Previously known as: apo-F; liver regeneration-related protein LRRG151; LOC500761; similar to apolipoprotein F
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr871,285,222 - 1,286,659 (+)NCBIGRCr8
mRatBN7.27700,688 - 702,130 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7700,762 - 701,946 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,456,982 - 3,458,436 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.075,332,963 - 5,334,417 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.075,635,788 - 5,637,242 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.072,689,501 - 2,690,938 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,689,501 - 2,690,936 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,668,375 - 2,669,812 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,562,515 - 1,563,953 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7576,977 - 578,414 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:22363685   PMID:28935895  


Genomics

Comparative Map Data
Apof
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr871,285,222 - 1,286,659 (+)NCBIGRCr8
mRatBN7.27700,688 - 702,130 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7700,762 - 701,946 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,456,982 - 3,458,436 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.075,332,963 - 5,334,417 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.075,635,788 - 5,637,242 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.072,689,501 - 2,690,938 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,689,501 - 2,690,936 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,668,375 - 2,669,812 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,562,515 - 1,563,953 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7576,977 - 578,414 (+)NCBICelera
Cytogenetic Map7q11NCBI
APOF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,360,568 - 56,362,857 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1256,360,568 - 56,362,857 (-)EnsemblGRCh38hg38GRCh38
GRCh371256,754,352 - 56,756,641 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361255,040,622 - 55,042,850 (-)NCBINCBI36Build 36hg18NCBI36
Build 341255,040,621 - 55,042,850NCBI
Celera1256,407,715 - 56,409,943 (-)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1253,793,395 - 53,795,623 (-)NCBIHuRef
CHM1_11256,721,725 - 56,723,953 (-)NCBICHM1_1
T2T-CHM13v2.01256,328,255 - 56,330,544 (-)NCBIT2T-CHM13v2.0
Apof
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,104,568 - 128,107,119 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10128,103,866 - 128,106,022 (+)EnsemblGRCm39 Ensembl
GRCm3810128,268,699 - 128,271,250 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,267,997 - 128,270,153 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710127,705,053 - 127,707,207 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610127,670,946 - 127,673,100 (+)NCBIMGSCv36mm8
Celera10130,653,807 - 130,655,961 (+)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1076.5NCBI
Apof
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554583,973,734 - 3,978,312 (-)NCBIChiLan1.0ChiLan1.0
APOF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21037,969,704 - 37,971,215 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11237,966,470 - 37,967,981 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01232,552,589 - 32,554,943 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11232,806,089 - 32,808,022 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,806,130 - 32,807,641 (+)Ensemblpanpan1.1panPan2
APOF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110661,400 - 666,125 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10661,875 - 662,927 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10724,984 - 729,288 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.010670,590 - 674,895 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10670,708 - 671,760 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110647,826 - 652,131 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.010890,982 - 895,287 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0101,014,707 - 1,019,012 (-)NCBIUU_Cfam_GSD_1.0
LOC101958515
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,104,056 - 58,105,719 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936646764,689 - 766,265 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APOF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,759,475 - 21,760,815 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,759,670 - 21,760,753 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2523,304,877 - 23,306,515 (-)NCBISscrofa10.2Sscrofa10.2susScr3
APOF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11152,316,413 - 52,318,956 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1152,316,800 - 52,318,659 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037193,666,840 - 193,669,111 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Apof
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480211,640,942 - 11,645,030 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Apof
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:87
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000041341
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat


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 appendage
High
Medium 29 29 29 1
Low 1 16 8 1 8 3 3 1 1 5 7 3
Below cutoff 2 11 12 4 18 4 5 6 12 14 11 4 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041341   ⟹   ENSRNOP00000049259
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl72,689,501 - 2,690,936 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094145
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7700,762 - 701,946 (+)Ensembl
RefSeq Acc Id: NM_001409538   ⟹   NP_001396467
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr871,285,222 - 1,286,659 (+)NCBI
mRatBN7.27700,688 - 702,130 (+)NCBI
RefSeq Acc Id: NR_176857
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr871,285,222 - 1,286,659 (+)NCBI
mRatBN7.27700,688 - 702,130 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001396467 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88170 (Get FASTA)   NCBI Sequence Viewer  
  AAP92630 (Get FASTA)   NCBI Sequence Viewer  
  EDL84878 (Get FASTA)   NCBI Sequence Viewer  
  Q5M889 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000049259   ⟸   ENSRNOT00000041341
RefSeq Acc Id: NP_001396467   ⟸   NM_001409538
- Peptide Label: precursor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5M889-F1-model_v2 AlphaFold Q5M889 1-308 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13694930
Promoter ID:EPDNEW_R5455
Type:initiation region
Name:Apof_1
Description:apolipoprotein F
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.072,689,454 - 2,689,514EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560713 AgrOrtholog
BioCyc Gene G2FUF-35381 BioCyc
Ensembl Genes ENSRNOG00000033619 Ensembl
  ENSRNOG00000062320 Ensembl
IMAGE_CLONE IMAGE:7322324 IMAGE-MGC_LOAD
InterPro APOF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:500761 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:108796 IMAGE-MGC_LOAD
NCBI Gene 500761 ENTREZGENE
PANTHER APOLIPOPROTEIN F UniProtKB/Swiss-Prot
  APOLIPOPROTEIN F UniProtKB/TrEMBL
  APOLIPOPROTEIN F UniProtKB/TrEMBL
  PTHR15011 UniProtKB/Swiss-Prot
Pfam Apolipo_F UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Apof PhenoGen
RatGTEx ENSRNOG00000033619 RatGTEx
  ENSRNOG00000062320 RatGTEx
UniProt A6KSB4_RAT UniProtKB/TrEMBL
  APOF_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q7TP25 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Apof  apolipoprotein F  LOC500761  similar to apolipoprotein F  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC500761  similar to apolipoprotein F      Symbol and Name status set to provisional 70820 PROVISIONAL