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HLA-F Gene(Protein Coding)

Major Histocompatibility Complex, Class I, F

GCID:
GC06P031332
GIFtS:
45
Genes Participants
UDN Logo

Aliases for HLA-F Gene

Aliases for HLA-F Gene

  • Major Histocompatibility Complex, Class I, F 2 3 5
  • MHC Class I Antigen F 3 4
  • Leukocyte Antigen F 3 4
  • HLA F Antigen 3 4
  • HLA-5.4 3 4
  • CDA12 3 4
  • HLAF 3 4
  • HLA Class I Histocompatibility Antigen, Alpha Chain F 3
  • HLA-CDA12 3

External Ids for HLA-F Gene

Previous GeneCards Identifiers for HLA-F Gene

  • GC06P029748
  • GC06P029461
  • GC06P029800
  • GC06P029801
  • GC06P029802
  • GC06P029690
  • GC06P029499
  • GC06P029853
  • GC06P030080
  • GC06P030326
  • GC06P030478
  • GC06P030678
  • GC06P030840
  • GC06P031001
  • GC06P031160

Summaries for HLA-F Gene

Entrez Gene Summary for HLA-F Gene

  • This gene belongs to the HLA class I heavy chain paralogues. It encodes a non-classical heavy chain that forms a heterodimer with a beta-2 microglobulin light chain, with the heavy chain anchored in the membrane. Unlike most other HLA heavy chains, this molecule is localized in the endoplasmic reticulum and Golgi apparatus, with a small amount present at the cell surface in some cell types. It contains a divergent peptide-binding groove, and is thought to bind a restricted subset of peptides for immune presentation. This gene exhibits few polymorphisms. Multiple transcript variants encoding different isoforms have been found for this gene. These variants lack a coding exon found in transcripts from other HLA paralogues due to an altered splice acceptor site, resulting in a shorter cytoplasmic domain. [provided by RefSeq, Jul 2008]

GeneCards Summary for HLA-F Gene

HLA-F (Major Histocompatibility Complex, Class I, F) is a Protein Coding gene. Among its related pathways are Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell and HTLV-I infection. Gene Ontology (GO) annotations related to this gene include signaling receptor binding and TAP1 binding. An important paralog of this gene is HLA-A.

UniProtKB/Swiss-Prot for HLA-F Gene

  • Involved in the presentation of foreign antigens to the immune system.

Gene Wiki entry for HLA-F Gene

Additional gene information for HLA-F Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HLA-F Gene

Genomics for HLA-F Gene

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GeneHancer (GH) Regulatory Elements for HLA-F Gene

Promoters and enhancers for HLA-F Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH06J029722 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 698.5 +1.8 1808 4.1 SMAD1 GLIS2 ZNF207 ZNF143 FOS NFYC REST NBN KDM1A HNF4A HLA-F HLA-J ZFP57 ZNRD1 HLA-H HCG4P5 IFITM4P HLA-F-AS1 DHX16 MICE
GH06J029708 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 35.7 -13.4 -13387 2.6 PKNOX1 CEBPB EBF1 MEF2B ATF2 IKZF1 CREB1 PRDM1 RUNX3 GC06M030390 ZDHHC20P1 HLA-F ZFP57 HLA-J IFITM4P HLA-H HCG4P5 ZNRD1ASP OR2H1
GH06J029963 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 16.3 +243.5 243474 4.8 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 HLA-A HLA-K HCG4P3 ZNRD1 HLA-W TRIM39 HLA-H PPP1R10 MDC1 DHX16
GH06J029728 Enhancer 0.6 ENCODE dbSUPER 22.7 +5.6 5646 0.3 NFATC1 MAFG NFE2L2 RPL23AP1 HLA-F HCG4P5 HCG9P5 HLA-F-AS1 GC06M029612
GH06J029789 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 9.2 +68.8 68793 3.9 CTCF PKNOX1 MAX RAD21 YY1 FOS EZH2 NR2F1 USF2 CEBPB HCG4 HLA-V HLA-H ZNRD1 HLA-A HLA-T ZNRD1ASP HCG4P3 ZFP57 TRIM31-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HLA-F on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HLA-F gene promoter:
  • ISGF-3
  • Ik-3
  • AML1a
  • p300
  • Zic3
  • HOXA5
  • GATA-2
  • Bach2
  • SREBP-1c
  • SREBP-1b

Genomic Locations for HLA-F Gene

Genomic Locations for HLA-F Gene
chr6:29,722,775-29,740,355
(GRCh38/hg38)
Size:
17,581 bases
Orientation:
Plus strand
chr6:29,690,552-29,706,305
(GRCh37/hg19)
Size:
15,754 bases
Orientation:
Plus strand

Genomic View for HLA-F Gene

Genes around HLA-F on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HLA-F Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HLA-F Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HLA-F Gene

Proteins for HLA-F Gene

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  • Protein details for HLA-F Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P30511-HLAF_HUMAN
    Recommended name:
    HLA class I histocompatibility antigen, alpha chain F
    Protein Accession:
    P30511
    Secondary Accessions:
    • Q5JQI8
    • Q5JQJ1
    • Q5SPT5
    • Q860R0
    • Q8MGQ1
    • Q8WLP5
    • Q95HC0
    • Q9TP68

    Protein attributes for HLA-F Gene

    Size:
    346 amino acids
    Molecular mass:
    39062 Da
    Quaternary structure:
    • Heterodimer of an alpha chain and a beta chain (beta-2-microglobulin).
    SequenceCaution:
    • Sequence=AAC24827.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=AAH09260.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAB63337.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAA34947.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAB46623.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HLA-F Gene

    Alternative splice isoforms for HLA-F Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HLA-F Gene

Protein Expression for HLA-F Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HLA-F Gene

  • Glycosylation at isoforms=2, 3107
  • Ubiquitination at isoforms=3264
  • Modification sites at PhosphoSitePlus

Other Protein References for HLA-F Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HLA-F Gene

Domains & Families for HLA-F Gene

Gene Families for HLA-F Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted membrane proteins

Protein Domains for HLA-F Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HLA-F Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P30511

UniProtKB/Swiss-Prot:

HLAF_HUMAN :
  • Belongs to the MHC class I family.
Family:
  • Belongs to the MHC class I family.
genes like me logo Genes that share domains with HLA-F: view

Function for HLA-F Gene

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Molecular function for HLA-F Gene

UniProtKB/Swiss-Prot Function:
Involved in the presentation of foreign antigens to the immune system.
GENATLAS Biochemistry:
HLA class Ib,44kDa,5.4kb HindIII fragment,TAP and tapasin dependent,expression at the cell surface,correlating with the binding of an MHC class I leader peptide (see MHC1)

Phenotypes From GWAS Catalog for HLA-F Gene

Gene Ontology (GO) - Molecular Function for HLA-F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding IBA --
GO:0005515 protein binding IPI 20483783
GO:0042605 peptide antigen binding IBA --
GO:0046978 TAP1 binding IPI 10605026
GO:0046979 TAP2 binding IPI 10605026
genes like me logo Genes that share ontologies with HLA-F: view
genes like me logo Genes that share phenotypes with HLA-F: view

Animal Model Products

CRISPR Products

miRNA for HLA-F Gene

miRTarBase miRNAs that target HLA-F

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HLA-F

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HLA-F Gene

Localization for HLA-F Gene

Subcellular locations from UniProtKB/Swiss-Prot for HLA-F Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HLA-F gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5
golgi apparatus 5
endosome 4
extracellular 2
mitochondrion 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for HLA-F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005783 endoplasmic reticulum IDA 10605026
GO:0005886 plasma membrane IBA,TAS --
GO:0009986 cell surface IDA 20865824
GO:0012507 ER to Golgi transport vesicle membrane TAS --
genes like me logo Genes that share ontologies with HLA-F: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HLA-F Gene

Pathways & Interactions for HLA-F Gene

genes like me logo Genes that share pathways with HLA-F: view

Interacting Proteins for HLA-F Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000259951%0d%0a9606.ENSP00000452780%0d%0a9606.ENSP00000270452%0d%0a9606.ENSP00000380073%0d%0a9606.ENSP00000360876%0d%0a9606.ENSP00000359504%0d%0a
Selected Interacting proteins: ENSP00000259951 P30511-HLAF_HUMAN for HLA-F Gene via STRING UniProtKB IID

Symbol External ID(s) Details
HLA-B
HLA-A
HLA-C
HLA-DRB1
HLA-E
GPS-Prot Interaction Network for HLA-F

Gene Ontology (GO) - Biological Process for HLA-F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002376 immune system process IEA --
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I TAS,IBA --
GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS --
GO:0002480 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent TAS --
GO:0050776 regulation of immune response TAS --
genes like me logo Genes that share ontologies with HLA-F: view

No data available for SIGNOR curated interactions for HLA-F Gene

Drugs & Compounds for HLA-F Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for HLA-F Gene

Products:

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  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for HLA-F Gene

(10) REFSEQ mRNAs :
(18) Additional mRNA sequences :
(23) Selected AceView cDNA sequences:
(15) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HLA-F Gene

Major histocompatibility complex, class I, F:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HLA-F

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HLA-F Gene

No ASD Table

Relevant External Links for HLA-F Gene

GeneLoc Exon Structure for
HLA-F
ECgene alternative splicing isoforms for
HLA-F

Expression for HLA-F Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HLA-F Gene

mRNA expression in normal human tissues for HLA-F Gene
mRNA expression by BioGPS for HLA-F GenemRNA expression by GTEx for HLA-F Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HLA-F Gene

This gene is overexpressed in Whole Blood (x9.1) and Spleen (x5.5).

Protein differential expression in normal tissues from HIPED for HLA-F Gene

This gene is overexpressed in Peripheral blood mononuclear cells (18.4), Skin (13.0), NK cells (8.9), and CD8 Tcells (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HLA-F Gene



Protein tissue co-expression partners for HLA-F Gene

- Elite partner

SOURCE GeneReport for Unigene cluster for HLA-F Gene:

Hs.519972

Evidence on tissue expression from TISSUES for HLA-F Gene

  • Lung(4.5)
  • Blood(2.1)
  • Spleen(2)
genes like me logo Genes that share expression patterns with HLA-F: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HLA-F Gene

Orthologs for HLA-F Gene

This gene was present in the common ancestor of mammals.

Orthologs for HLA-F Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PATR-F 33
  • 98.16 (n)
PATR-AL 34
  • 72 (a)
 ManyToMany
dog
(Canis familiaris)
 Mammalia DLA-79 33
  • 77.47 (n)
mouse
(Mus musculus)
 Mammalia Gm7030 16 33
  • 74.52 (n)
Species where no ortholog for HLA-F was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for HLA-F Gene

ENSEMBL:
Gene Tree for HLA-F (if available)
TreeFam:
Gene Tree for HLA-F (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HLA-F: view image

Paralogs for HLA-F Gene

Paralogs for HLA-F Gene

(116) SIMAP similar genes for HLA-F Gene using alignment to 14 proteins:

  • HLAF_HUMAN
  • D0EV57_HUMAN
  • E9PGX5_HUMAN
  • F6T2Q8_HUMAN
  • H0Y4J4_HUMAN
  • H0Y842_HUMAN
  • O78094_HUMAN
  • Q54A71_HUMAN
  • Q5JZ48_HUMAN
  • Q6DU20_HUMAN
  • Q6DU28_HUMAN
  • Q7YP62_HUMAN
  • Q861E9_HUMAN
  • Q861F0_HUMAN

Pseudogenes.org Pseudogenes for HLA-F Gene

genes like me logo Genes that share paralogs with HLA-F: view

Variants for HLA-F Gene

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Sequence variations from dbSNP and Humsavar for HLA-F Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000094516 -- 29,729,008(+) G/C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1000962638 -- 29,731,494(+) A/G genic_downstream_transcript_variant, intron_variant
rs1001133955 -- 29,727,200(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1001467883 -- 29,731,266(+) T/C genic_downstream_transcript_variant, intron_variant
rs1001519169 -- 29,728,097(+) T/A/C coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant, stop_gained, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for HLA-F Gene

Variant ID Type Subtype PubMed ID
dgv992e201 CNV deletion 23290073
esv25966 CNV gain+loss 19812545
nsv1074389 CNV deletion 25765185
nsv10809 CNV gain 18304495
nsv1122126 CNV deletion 24896259
nsv1144137 CNV deletion 24896259
nsv428139 CNV gain 18775914
nsv462673 CNV loss 19166990
nsv508397 CNV deletion 20534489
nsv601230 CNV loss 21841781
nsv970101 CNV duplication 23825009

Variation tolerance for HLA-F Gene

Residual Variation Intolerance Score: 79.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.80; 83.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HLA-F Gene

Human Gene Mutation Database (HGMD)
HLA-F
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HLA-F

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HLA-F Gene

Disorders for HLA-F Gene

Additional Disease Information for HLA-F

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HLA-F Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HLA-F Gene

Publications for HLA-F Gene

  1. Human leukocyte antigen F (HLA-F). An expressed HLA gene composed of a class I coding sequence linked to a novel transcribed repetitive element. (PMID: 1688605) Geraghty DE … Koller BH (The Journal of experimental medicine 1990) 2 3 4 22 58
  2. Genetic associations of common deletion polymorphisms in families with Avellino corneal dystrophy. (PMID: 19622345) Park M … Kim HL (Biochemical and biophysical research communications 2009) 3 22 44 58
  3. SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians. (PMID: 17971048) Burfoot RK … Rubio JP (Tissue antigens 2008) 3 22 44 58
  4. HLA-E, HLA-F, and HLA-G polymorphism: genomic sequence defines haplotype structure and variation spanning the nonclassical class I genes. (PMID: 16570139) Pyo CW … Geraghty DE (Immunogenetics 2006) 3 4 22 58
  5. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree BA … IMSGC (PloS one 2010) 3 44 58

Products for HLA-F Gene

Sources for HLA-F Gene

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