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Aliases for HLA-F Gene

Aliases for HLA-F Gene

  • Major Histocompatibility Complex, Class I, F 2 3
  • HLAF 3 4 6
  • MHC Class I Antigen F 3 4
  • Leukocyte Antigen F 3 4
  • HLA F Antigen 3 4
  • HLA-CDA12 3 6
  • HLA-5.4 3 4
  • CDA12 3 4
  • HLA Class I Histocompatibility Antigen, Alpha Chain F 3
  • HLA Class I Molecule 3
  • MHC Class Ib Antigen 3

External Ids for HLA-F Gene

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. Diseases associated with HLA-F include hiv-1. Among its related pathways are Class I MHC mediated antigen processing and presentation and Actin Nucleation by ARP-WASP Complex. GO annotations related to this gene include receptor binding and peptide antigen binding. An important paralog of this gene is MR1.

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

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

Genomics for HLA-F Gene

Genomic Location for HLA-F Gene

29,722,775 bp from pter
29,738,528 bp from pter
15,754 bases
Plus strand

Genomic View for HLA-F Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HLA-F Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Regulatory Elements for HLA-F Gene

Proteins for HLA-F Gene

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

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

    Protein attributes for HLA-F Gene

    346 amino acids
    Molecular mass:
    39062 Da
    Quaternary structure:
    • Heterodimer of an alpha chain and a beta chain (beta-2-microglobulin)
    • 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};

    Alternative splice isoforms for HLA-F Gene


neXtProt entry for HLA-F Gene

Proteomics data for HLA-F Gene at MOPED

Post-translational modifications for HLA-F Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys197 and Lys264
  • Glycosylation at Asn107

Other Protein References for HLA-F Gene

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

Domains for HLA-F Gene

Gene Families for HLA-F Gene

  • C1SET :Immunoglobulin superfamily / C1-set domain containing
  • HLA :Histocompatibility complex


  • Contains 1 Ig-like C1-type (immunoglobulin-like) domain.:
    • P30511
  • Belongs to the MHC class I family.:
    • P30511
genes like me logo Genes that share domains with HLA-F: view

Function for HLA-F Gene

Molecular function for HLA-F Gene

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)
UniProtKB/Swiss-Prot Function: Involved in the presentation of foreign antigens to the immune system

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

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding IBA --
GO:0005515 protein binding --
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

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting 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

Jensen Localization Image for HLA-F Gene COMPARTMENTS Subcellular localization image for HLA-F gene
Compartment Confidence
endoplasmic reticulum 4
endosome 4
golgi apparatus 4
plasma membrane 4
lysosome 1
mitochondrion 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 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

Pathways for HLA-F Gene

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

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

GO ID Qualified GO term Evidence PubMed IDs
GO:0001916 positive regulation of T cell mediated cytotoxicity IEA --
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I TAS --
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:0006955 immune response --
genes like me logo Genes that share ontologies with HLA-F: view

Transcripts for HLA-F Gene

Unigene Clusters for HLA-F Gene

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

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
ECgene alternative splicing isoforms for

Expression for HLA-F Gene

mRNA expression in normal human tissues 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 (9.1) and Spleen (5.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HLA-F Gene

SOURCE GeneReport for Unigene cluster for HLA-F Gene Hs.519972

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

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
(Pan troglodytes)
Mammalia PATR-AL 37
  • 72 (a)
  • 98.16 (n)
  • 97.97 (a)
(Canis familiaris)
Mammalia DLA-79 36
  • 77.47 (n)
  • 66.36 (a)
(Mus musculus)
Mammalia Gm11127 16
Gm7030 36
  • 74.52 (n)
  • 67.57 (a)
Species with no ortholog for HLA-F:
  • 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

Gene Tree for HLA-F (if available)
Gene Tree for HLA-F (if available)

Paralogs for HLA-F Gene

Paralogs for HLA-F Gene

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

Variants for HLA-F Gene

Sequence variations from dbSNP and Humsavar for HLA-F Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs1362125 -- 29,723,313(-) CAGGA(A/T)GAAGG upstream-variant-2KB
rs1362126 -- 29,723,242(-) AGCCT(C/T)CCAAC upstream-variant-2KB
rs1632952 -- 29,724,656(-) TCAGA(A/C/G)ATTTC intron-variant
rs1632953 -- 29,724,528(-) TTGGG(C/T)CCACT intron-variant
rs1632954 -- 29,723,614(-) TCCGG(A/G)GGCGG intron-variant

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

Variant ID Type Subtype PubMed ID
esv25966 CNV Gain+Loss 19812545
nsv428139 CNV Gain 18775914
nsv508397 CNV Loss 20534489
dgv1039e201 CNV Deletion 23290073
nsv462673 CNV Loss 19166990
nsv883531 CNV Loss 21882294
nsv10809 CNV Gain 18304495

Relevant External Links for HLA-F Gene

HapMap Linkage Disequilibrium report
Locus Specific Mutation Databases (LSDB)

Disorders for HLA-F Gene

(1) MalaCards Diseases for HLA-F Gene

Search for HLA-F Gene in MalaCards »

(1) University of Copenhagen DISEASES for HLA-F Gene

Relevant External Links for HLA-F

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with HLA-F: view

No data available for UniProtKB/Swiss-Prot 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 D.E. … Koller B.H. (J. Exp. Med. 1990) 2 3 4 23
  2. HLA-E, HLA-F, and HLA-G polymorphism: genomic sequence defines haplotype structure and variation spanning the nonclassical class I genes. (PMID: 16570139) Pyo C.W. … Geraghty D.E. (Immunogenetics 2006) 3 4 23
  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 R.K. … Rubio J.P. (Tissue Antigens 2008) 3 23 49
  4. Genetic associations of common deletion polymorphisms in families with Avellino corneal dystrophy. (PMID: 19622345) Park M. … Kim H.L. (Biochem. Biophys. Res. Commun. 2009) 3 23 49
  5. HLA-F surface expression on B cell and monocyte cell lines is partially independent from tapasin and completely independent from TAP. (PMID: 14607927) Lee N. … Geraghty D.E. (J. Immunol. 2003) 3 23

Products for HLA-F Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate HLA-F
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for HLA-F
    • Block miRNA regulation of HLA-F using miScript Target Protectors

    Sources for HLA-F Gene

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