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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

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 Interferon gamma signaling and HTLV-I infection. GO annotations related to this gene include 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

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

Genomics for HLA-F Gene

Regulatory Elements for HLA-F Gene

Enhancers for HLA-F Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F029722 0.7 ENCODE 48.5 +1.8 1808 4.1 ATF1 WRNIP1 SIN3A GLIS2 CBX5 ZNF143 ZNF207 FOS ZNF263 NFYC HLA-F HLA-J ZFP57 HLA-H HCG4P5 IFITM4P HLA-F-AS1 DHX16 MICE HCG4P7
GH06F029708 0.9 FANTOM5 Ensembl ENCODE 35.7 -13.4 -13388 2.6 PKNOX1 BHLHE40 CEBPB CEBPG EBF1 ATF2 IKZF1 PRDM1 TRIM28 HLA-F ZFP57 HLA-J IFITM4P HLA-H HCG4P5 ZNRD1ASP OR2H1 HLA-A HLA-K
GH06F029728 0.2 ENCODE 22.7 +5.6 5646 0.3 POLR2A MAFG CHD7 NFE2L2 HLA-F HCG4P5 RPL23AP1 HCG9P5
GH06F029963 1.6 FANTOM5 Ensembl ENCODE 16.3 +243.5 243475 4.8 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ZFP64 ARID4B SIN3A FEZF1 HLA-A HLA-W HLA-K MICD HLA-H HLA-J HCG4P5 HCG4 IFITM4P ABCF1
GH06F029705 0.2 ENCODE 15.8 -17.0 -16957 0.2 CTCF ZNF654 ETV1 TRIM22 REST ZIC2 RAD21 RFX5 ZNF366 IKZF1 HLA-F ZFP57 HLA-H HLA-W ZDHHC20P1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

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

Promoters for HLA-F Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000487553 1025 2401 TBP ATF1 WRNIP1 ZNF76 SIN3A RFX5 GLIS2 ZNF366 ZNF143 ZNF207

Genomic Location for HLA-F Gene

Chromosome:
6
Start:
29,722,775 bp from pter
End:
29,740,355 bp from pter
Size:
17,581 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 StructureGene Density

Proteins for HLA-F Gene

  • 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};

    Alternative splice isoforms for HLA-F Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HLA-F Gene

Post-translational modifications for HLA-F Gene

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

Domains & Families for HLA-F Gene

Graphical View of Domain Structure for InterPro Entry

P30511

UniProtKB/Swiss-Prot:

HLAF_HUMAN :
  • Contains 1 Ig-like C1-type (immunoglobulin-like) domain.
  • Belongs to the MHC class I family.
Domain:
  • Contains 1 Ig-like C1-type (immunoglobulin-like) domain.
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

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: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

Phenotypes for HLA-F Gene

GenomeRNAi human phenotypes for HLA-F:
genes like me logo Genes that share phenotypes with HLA-F: view

Animal Model Products

miRNA for HLA-F Gene

miRTarBase miRNAs that target HLA-F

Flow Cytometry 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
Jensen Localization Image for HLA-F Gene COMPARTMENTS Subcellular localization image for HLA-F gene
Compartment Confidence
plasma membrane 3
extracellular 2
cytosol 1
endoplasmic reticulum 1
golgi apparatus 1
lysosome 1
mitochondrion 1
vacuole 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 & 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 4 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000259951%0d%0a9606.ENSP00000452780%0d%0a9606.ENSP00000375629%0d%0a9606.ENSP00000315997%0d%0a9606.ENSP00000346206%0d%0a
Selected Interacting proteins: P30511-HLAF_HUMAN ENSP00000259951 for HLA-F Gene via IID STRING

Symbol External ID(s) Details
HLA-B
HLA-A
HLA-C
HLA-DRB1
B2M

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 --
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

Transcripts for HLA-F Gene

Unigene Clusters for HLA-F Gene

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

Flow Cytometry 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

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 (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, PaxDb, 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
genes like me logo Genes that share expression patterns with HLA-F: view

No data available for mRNA Expression by UniProt/SwissProt 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 34
  • 98.16 (n)
PATR-AL 35
  • 72 (a)
ManyToMany
dog
(Canis familiaris)
Mammalia DLA-79 34
  • 77.47 (n)
mouse
(Mus musculus)
Mammalia Gm7030 34 16
  • 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)

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
rs10456054 -- 29,722,404(+) gtagt(C/T)tcagc upstream-variant-2KB
rs10542672 -- 29,735,360(+) ATATA(-/TGTGTG)TATAT intron-variant
rs1059174 -- 29,726,650(-) GGCTA(A/G)TTCCA intron-variant, nc-transcript-variant, downstream-variant-500B
rs10645673 -- 29,731,524(+) AGATT(-/GA)GAGAG intron-variant
rs10947008 -- 29,735,373(+) TATAT(A/T)TATAT intron-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)

Relevant External Links for HLA-F Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HLA-F

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

Disorders for HLA-F Gene

Relevant External Links for HLA-F

Genetic Association Database (GAD)
HLA-F
Human Genome Epidemiology (HuGE) Navigator
HLA-F
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HLA-F

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 D.E. … Koller B.H. (J. Exp. Med. 1990) 2 3 4 22 64
  2. 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 22 46 64
  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 22 46 64
  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 C.W. … Geraghty D.E. (Immunogenetics 2006) 3 4 22 64
  5. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree B.A. … . (PLoS ONE 2010) 3 46 64

Products for HLA-F Gene

Sources for HLA-F Gene

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