APOF (apolipoprotein F) - Rat Genome Database

Name: APOF
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: APOF (apolipoprotein F) Sus scrofa

Analyze

Symbol:

APOF

Name:

apolipoprotein F

RGD ID:

14064380

Description:

INVOLVED IN cholesterol efflux (ortholog); cholesterol metabolic process (ortholog); triglyceride metabolic process (ortholog); ASSOCIATED WITH hepatocellular carcinoma (ortholog); FOUND IN extracellular space (inferred); INTERACTS WITH deoxynivalenol

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

APON; ovarian and testicular apolipoprotein N

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	APOF (apolipoprotein F)	HGNC	Ensembl, NCBI, Treefam
Mus musculus (house mouse):	Apof (apolipoprotein F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Apof (apolipoprotein F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Apof (apolipoprotein F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	APOF (apolipoprotein F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	APOF (apolipoprotein F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101958515 (apolipoprotein F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	APOF (apolipoprotein F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Apof (apolipoprotein F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	21,759,475 - 21,760,815 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	21,759,670 - 21,760,753 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	23,304,877 - 23,306,515 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

hepatocellular carcinoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

deoxynivalenol (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cholesterol efflux (ISO)

cholesterol metabolic process (IBA,IEA,ISO)

triglyceride metabolic process (ISO)

Cellular Component

extracellular space (IBA,IEA)

References

Additional References at PubMed

PMID:14681463	PMID:15256496	PMID:17145712	PMID:30032202

Genomics

Comparative Map Data

APOF
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	21,759,475 - 21,760,815 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	21,759,670 - 21,760,753 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	23,304,877 - 23,306,515 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

APOF
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	56,360,568 - 56,362,857 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	56,360,568 - 56,362,857 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	56,754,352 - 56,756,641 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	55,040,622 - 55,042,850 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	55,040,621 - 55,042,850	NCBI
Celera	12	56,407,715 - 56,409,943 (-)	NCBI		Celera
Cytogenetic Map	12	q13.3	NCBI
HuRef	12	53,793,395 - 53,795,623 (-)	NCBI		HuRef
CHM1_1	12	56,721,725 - 56,723,953 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	12	56,328,255 - 56,330,544 (-)	NCBI		T2T-CHM13v2.0

Apof
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	128,104,568 - 128,107,119 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	10	128,103,866 - 128,106,022 (+)	Ensembl		GRCm39 Ensembl
GRCm38	10	128,268,699 - 128,271,250 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	128,267,997 - 128,270,153 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	127,705,053 - 127,707,207 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	10	127,670,946 - 127,673,100 (+)	NCBI		MGSCv36	mm8
Celera	10	130,653,807 - 130,655,961 (+)	NCBI		Celera
Cytogenetic Map	10	D3	NCBI
cM Map	10	76.5	NCBI

Apof
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	1,285,222 - 1,286,659 (+)	NCBI		GRCr8
mRatBN7.2	7	700,688 - 702,130 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	700,762 - 701,946 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	3,456,982 - 3,458,436 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	5,332,963 - 5,334,417 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	5,635,788 - 5,637,242 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	2,689,501 - 2,690,938 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	2,689,501 - 2,690,936 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	2,668,375 - 2,669,812 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	1,562,515 - 1,563,953 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	7	576,977 - 578,414 (+)	NCBI		Celera
Cytogenetic Map	7	q11	NCBI

Apof
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955458	3,973,734 - 3,978,312 (-)	NCBI	ChiLan1.0	ChiLan1.0

APOF
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	10	37,969,704 - 37,971,215 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	37,966,470 - 37,967,981 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	32,552,589 - 32,554,943 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	32,806,089 - 32,808,022 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	32,806,130 - 32,807,641 (+)	Ensembl	panpan1.1		panPan2

APOF
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	661,400 - 666,125 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	661,875 - 662,927 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	724,984 - 729,288 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	670,590 - 674,895 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	670,708 - 671,760 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	647,826 - 652,131 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	890,982 - 895,287 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	1,014,707 - 1,019,012 (-)	NCBI		UU_Cfam_GSD_1.0

LOC101958515
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	58,104,056 - 58,105,719 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936646	764,689 - 766,265 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

APOF
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	11	52,316,413 - 52,318,956 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	52,316,800 - 52,318,659 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	193,666,840 - 193,669,111 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Apof
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624802	11,640,942 - 11,645,030 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in APOF
20 total Variants

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	hemolymphoid system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system
High
Medium
Low	9	2	3	5	1	5		1	1
Below cutoff		1			1	6	2		2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001003925	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000033	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK232481	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK233564	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK346024	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK346179	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY583018	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CU655980	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSSCT00000000430 ⟹ ENSSSCP00000000424

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1 Ensembl	5	21,759,475 - 21,760,815 (-)	Ensembl

RefSeq Acc Id:

ENSSSCT00000080029 ⟹ ENSSSCP00000060852

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1 Ensembl	5	21,750,067 - 21,751,157 (-)	Ensembl

RefSeq Acc Id:

NM_001003925 ⟹ NP_001003925

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	5	21,759,670 - 21,760,753 (-)	NCBI

Sequence:

show sequence

ATTTACATCAGGGAAGCACCAGGGCAAAGGACGTGTTTAGACCATCTCATTCCTCCGGCTTGTT
TTTTTCTGGAGCAAGGCTGTTTTGCAAACCCACCATGATCCAGACTGAGCTGCTCTTTTGCTGT
GTCTTGCTGTCCTCGGTGACTGCCTTTCCAAGAAGTGCCCAAGAAGGGGCCCTGACCTTCCAGC
CACCTTTCACAGAAACTGGGGGTCCTCTGGACATGCTCTCCAATCAGATCTCTCTCCCAGATCC
CAAGATGTGTCAGGATCTCTTGCACGTGGTCCCCTCCTTAGCCCCTCTGCCTGAGTACCTATCC
AACTTAGCTCTGGAGGTGGCCCTGGAGGAGGTCGGCTGCCTGACTGAGGCCCACATGCTGGAAC
TTCAGCTTGTTAAGATGGGAGGAAAGGACACCACTGAAACCCTCATCCGTGAGAGCAAAAAGCG
CAATGAAGAAAAAGGGATCAACGATGGTGAGATCATGCTGAGGGGTCTAGAAGGATCCCCGGGG
GAGCTTAGGCGGGTCCAGCGCTCAGTTACCCTTCCTGAGGCATGTCAGCAGGAGGGTAGATGGG
TGCTCTACGAGCTAGCAGAACTGATAGGTGAGTTTGCTGAGAAGCTCCCTTCCACTGAGCTGGT
AAGAGAGTTAAAGACAGCTGCTGTTGATGTCACCCAGAAGTGCACAGATGAGTCCTGGCAGCAT
TTGGAAGCAGTAGGCAATCGGTTGATGAAAAACCCTGAGACCAAAGATTTCACAATGCCTATGG
ACGATCAGATATACTTTGTCAAGCGTTCTGTAGCCATTCTGGCACGTGTTATACTGGAATTCAT
ACAGAAATATTTCCAGGAGTTTTTTGGATAGGGAAGCCCTCTGAGGCATCATATTTCCTTTCTC
AAATGTCTCTAAAAGACATGTGACTAGAGTCAGCTTTGCTAGCTCT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001003925	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAT95402	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSSCP00000000424
	ENSSSCP00000000424.2
	ENSSSCP00005021450.1
	ENSSSCP00015025713.1
	ENSSSCP00025019662.1
	ENSSSCP00030018656.1
	ENSSSCP00035003242.1
	ENSSSCP00040002666.1
	ENSSSCP00045028493.1
	ENSSSCP00050040836.1
	ENSSSCP00055016916.1
	ENSSSCP00060048164.1
	ENSSSCP00065040062.1

RefSeq Acc Id:	NP_001003925 ⟸ NM_001003925
- Peptide Label:	precursor
- UniProtKB:	Q68RU1 (UniProtKB/TrEMBL), A0A8D1I4L7 (UniProtKB/TrEMBL), A0A8D0J103 (UniProtKB/TrEMBL)
- Sequence:	show sequence MIQTELLFCCVLLSSVTAFPRSAQEGALTFQPPFTETGGPLDMLSNQISLPDPKMCQDLLHVVP SLAPLPEYLSNLALEVALEEVGCLTEAHMLELQLVKMGGKDTTETLIRESKKRNEEKGINDGEI MLRGLEGSPGELRRVQRSVTLPEACQQEGRWVLYELAELIGEFAEKLPSTELVRELKTAAVDVT QKCTDESWQHLEAVGNRLMKNPETKDFTMPMDDQIYFVKRSVAILARVILEFIQKYFQEFFG hide sequence

RefSeq Acc Id:

ENSSSCP00000000424 ⟸ ENSSSCT00000000430

RefSeq Acc Id:

ENSSSCP00000060852 ⟸ ENSSSCT00000080029

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00000000398	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCG00000048087	Ensembl
	ENSSSCG00005022301	UniProtKB/TrEMBL
	ENSSSCG00015048251	UniProtKB/TrEMBL
	ENSSSCG00025033770	UniProtKB/TrEMBL
	ENSSSCG00030029398	UniProtKB/TrEMBL
	ENSSSCG00035007736	UniProtKB/TrEMBL
	ENSSSCG00040005027	UniProtKB/TrEMBL
	ENSSSCG00045024057	UniProtKB/TrEMBL
	ENSSSCG00050069440	UniProtKB/TrEMBL
	ENSSSCG00055010881	UniProtKB/TrEMBL
	ENSSSCG00060078348	UniProtKB/TrEMBL
	ENSSSCG00065066617	UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00000000430	ENTREZGENE
	ENSSSCT00000000430.5	UniProtKB/TrEMBL
	ENSSSCT00005035216.1	UniProtKB/TrEMBL
	ENSSSCT00015064270.1	UniProtKB/TrEMBL
	ENSSSCT00025045992.1	UniProtKB/TrEMBL
	ENSSSCT00030040911.1	UniProtKB/TrEMBL
	ENSSSCT00035009626.1	UniProtKB/TrEMBL
	ENSSSCT00040006672.1	UniProtKB/TrEMBL
	ENSSSCT00045041032.1	UniProtKB/TrEMBL
	ENSSSCT00050094734.1	UniProtKB/TrEMBL
	ENSSSCT00055021357.1	UniProtKB/TrEMBL
	ENSSSCT00060108185.1	UniProtKB/TrEMBL
	ENSSSCT00065091450.1	UniProtKB/TrEMBL
InterPro	APOF	UniProtKB/TrEMBL
KEGG Report	ssc:445462	UniProtKB/TrEMBL
NCBI Gene	APOF	ENTREZGENE
PANTHER	APOLIPOPROTEIN N	UniProtKB/TrEMBL
	PTHR15011	UniProtKB/TrEMBL
Pfam	Apolipo_F	UniProtKB/TrEMBL
UniProt	A0A8D0J103	ENTREZGENE, UniProtKB/TrEMBL
	A0A8D1I4L7	ENTREZGENE, UniProtKB/TrEMBL
	Q68RU1	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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