Human Gene HLA-F (uc011gpw.1) Description and Page Index
  Description: Homo sapiens major histocompatibility complex, class I, F (HLA-F), transcript variant 1, mRNA.
RefSeq Summary (NM_018950): 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].
Transcript (Including UTRs)
   Position: chr6_mann_hap4:991,622-997,613 Size: 5,992 Total Exon Count: 8 Strand: +
Coding Region
   Position: chr6_mann_hap4:991,746-996,390 Size: 4,645 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDMicroarray
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated: 2013-06-14

+  Sequence and Links to Tools and Databases
  Press "+" in the title bar above to open this section.

-  Comments and Description Text from UniProtKB
  ID: B4DQ99_HUMAN
DESCRIPTION: SubName: Full=cDNA FLJ60325, highly similar to HLA class I histocompatibility antigen, alpha chain F;
SIMILARITY: Belongs to the MHC class I family.
SIMILARITY: Contains Ig-like C1-type (immunoglobulin-like) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database: HLA-F
CDC HuGE Published Literature: HLA-F
Positive Disease Associations: Behcet Syndrome
Related Studies:
  1. Behcet Syndrome
    Elaine F Remmers et al. Nature genetics 2010, , Nature genetics. [PubMed 20622878]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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GNF Expression Atlas 1 Human Data on Affy U95 Chips

      
    
     
      
    
    
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.50124-0.286 Picture PostScript Text
3' UTR -353.151223-0.289 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007110 - Ig-like_dom
IPR013783 - Ig-like_fold
IPR003006 - Ig/MHC_CS
IPR003597 - Ig_C1-set
IPR011161 - MHC_I-like_Ag-recog
IPR011162 - MHC_I/II-like_Ag-recog
IPR027648 - MHC_I_a
IPR001039 - MHC_I_a_a1/a2

Pfam Domains:
PF00047 - Immunoglobulin domain
PF00129 - Class I Histocompatibility antigen, domains alpha 1 and 2
PF07654 - Immunoglobulin C1-set domain

SCOP Domains:
48726 - Immunoglobulin
54452 - MHC antigen-recognition domain

ModBase Predicted Comparative 3D Structure on B4DQ99
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK096962 - Homo sapiens cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F precursor.
X13112 - Human partial mRNA for MHC class I antigen HLA-A11K.
AK300090 - Homo sapiens cDNA FLJ60056 complete cds, highly similar to HLA class I histocompatibility antigen, alpha chain F precursor.
AK302420 - Homo sapiens cDNA FLJ53112 complete cds, highly similar to HLA class I histocompatibility antigen, alpha chain F precursor.
BC009260 - Homo sapiens major histocompatibility complex, class I, F, mRNA (cDNA clone IMAGE:4039990), partial cds.
AK309156 - Homo sapiens cDNA, FLJ99197.
AK303670 - Homo sapiens cDNA FLJ53123 complete cds.
AK298704 - Homo sapiens cDNA FLJ60325 complete cds, highly similar to HLA class I histocompatibility antigen, alpha chain F precursor.
AK125274 - Homo sapiens cDNA FLJ43284 fis, clone LYMPB2000083, highly similar to HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN F PRECURSOR.
AK225185 - Homo sapiens mRNA for major histocompatibility complex, class I, F precursor variant, clone: COL01957.
AK301488 - Homo sapiens cDNA FLJ54780 complete cds, highly similar to HLA class I histocompatibility antigen, alpha chain F precursor.
BC062991 - Homo sapiens major histocompatibility complex, class I, F, mRNA (cDNA clone MGC:74962 IMAGE:5496696), complete cds.
CU687616 - Synthetic construct Homo sapiens gateway clone IMAGE:100021717 5' read HLA-F mRNA.
AB590981 - Synthetic construct DNA, clone: pFN21AE1907, Homo sapiens HLA-F gene for major histocompatibility complex, class I, F, without stop codon, in Flexi system.
AY253269 - Homo sapiens MHC class Ib antigen (HLA-F) mRNA, HLA-F*0101 variant 1 allele, complete cds.
AY253270 - Homo sapiens MHC class Ib antigen (HLA-F) mRNA, HLA-F*0101 variant 2 allele, complete cds.
AY253271 - Homo sapiens MHC class Ib antigen (HLA-F) mRNA, HLA-F*0101 variant 3 allele, complete cds.
DQ367723 - Homo sapiens MHC class I antigen (HLA-F) mRNA, complete cds.
GQ891552 - Homo sapiens MHC class I antigen (HLA-F) mRNA, HLA-F*0109 allele, complete cds.
AY216682 - Homo sapiens nonclassical MHC class I antigen (HLA-F) mRNA, HLA-F*0101 variant allele, partial cds.
AY221102 - Homo sapiens MHC class I antigen (HLA-F) mRNA, partial cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis
hsa04514 - Cell adhesion molecules (CAMs)
hsa04612 - Antigen processing and presentation
hsa04650 - Natural killer cell mediated cytotoxicity
hsa04940 - Type I diabetes mellitus
hsa05320 - Autoimmune thyroid disease
hsa05330 - Allograft rejection
hsa05332 - Graft-versus-host disease
hsa05416 - Viral myocarditis

-  Other Names for This Gene
  Alternate Gene Symbols: AK298704, B4DQ99, B4DQ99_HUMAN, NM_018950, NP_061823
UCSC ID: uc011gpw.1
RefSeq Accession: NM_018950
Protein: B4DQ99

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK298704.1
exon count: 8CDS single in 3' UTR: no RNA size: 1533
ORF size: 1308CDS single in intron: no Alignment % ID: 99.87
txCdsPredict score: 2741.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 7
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.