Human Gene HLA-A (uc011gqw.2) Description and Page Index
  Description: Homo sapiens major histocompatibility complex, class I, A (HLA-A), transcript variant 1, mRNA.
RefSeq Summary (NM_002116): HLA-A belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from the endoplasmic reticulum lumen. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. Hundreds of HLA-A alleles have been described. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: chr6_mann_hap4:1,202,632-1,205,459 Size: 2,828 Total Exon Count: 6 Strand: +
Coding Region
   Position: chr6_mann_hap4:1,202,716-1,205,458 Size: 2,743 Coding Exon Count: 6 

Page IndexSequence and LinksGenetic AssociationsCTDMicroarrayRNA Structure
Other SpeciesmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

+  Sequence and Links to Tools and Databases
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-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database: HLA-A
CDC HuGE Published Literature: HLA-A
Positive Disease Associations: age , alopecia areata , Alzheimer's Disease , ANCA positive patients , Carbamazepine , Dengue , dermatitis, atopic , diabetes, type 1 , endometriosis , Enterovirus Infections , graft-versus-host disease , hepatitis C, chronic , hepatitis, fulminant non-A, nonB , HIV , HIV-1 control , leukemia , multiple sclerosis , nasopharyngeal cancer , nasopharyngeal carcinoma , pancreatitis, autoimmune; pancreatitis, chronic calcifying , periodontitis , prostate cancer , psoriasis , pulmonary hypertension; thrombosis, deep vein; pulmonary thromboembolism , schizophrenia , Sjogren's syndrome , Spondylarthropathies , vitiligo
Related Studies:
  1. age
    Poncet D et al. 1981, HLA-A2 and type 2 (insulin independent) diabetes mellitus in Pima Indians: an association of allele frequency with age., Diabetologia. 1981 Nov;21(5):460-3. [PubMed 7297796]
  2. alopecia areata
    Xiao, F. L. et al. 2005, Association of HLA class I alleles with aloplecia areata in Chinese Hans., Journal of dermatological science. 2006 Feb;41(2):109-19. [PubMed 16185849]
    This study demonstrated the positive association of HLA class I alleles and haplotypes with AA. There may be differences in genetic background in patients with different age of onset, grade of scalp hair loss, duration of current attack, a past history and a family history.
  3. alopecia areata
    Xiao, F. L. et al. 2005, Association of HLA class I alleles with aloplecia areata in Chinese Hans., Journal of dermatological science 2006 41- 2 : 109-19. [PubMed 16185849]
           more ... click here to view the complete list

-  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 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 -22.7084-0.270 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.

-  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
  M12758 - Human MHC class I HLA-A24 glycoprotein mRNA (exons 4,6-8), clone 1.
M64256 - Human MHC class I HLA-B mRNA, partial cds.
X13112 - Human partial mRNA for MHC class I antigen HLA-A11K.
AY786586 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*11new allele, complete cds, alternatively spliced.
AY786587 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*110101 allele, complete cds, alternatively spliced.
DQ336694 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*110101 allele, complete cds.
L18898 - Human HLA lymphocyte antigen (HLA A*8001) mRNA, complete cds.
U25971 - Human MHC class I antigen HLA-A2407 (HLA-A) mRNA, complete cds.
Y17224 - Homo sapiens mRNA for MHC class I antigen, allele A*1103.
U43334 - Human MHC class I antigen HLA-A mRNA, partial cds.
M27971 - Human MHC class I HLA-ABC mRNA, 3' end.
D32130 - Homo sapiens HLA-A26 mRNA for HLA class-I heavy chain, complete cds.
D32131 - Homo sapiens HLA-A mRNA for MHC class I antigen, complete cds, HLA-A26, clone:cMIY-3.
AK316195 - Homo sapiens cDNA, FLJ79094 complete cds, highly similar to HLA class I histocompatibility antigen, A-30alpha chain precursor.
AK310846 - Homo sapiens cDNA, FLJ17888.
AK309533 - Homo sapiens cDNA, FLJ99574.
AK301014 - Homo sapiens cDNA FLJ51109 complete cds, highly similar to HLA class I histocompatibility antigen, A-3 alpha chain precursor.
AK316198 - Homo sapiens cDNA, FLJ79097 complete cds, highly similar to HLA class I histocompatibility antigen, A-30alpha chain precursor.
AK310047 - Homo sapiens cDNA, FLJ17089.
AK313119 - Homo sapiens cDNA, FLJ93604, highly similar to Homo sapiens major histocompatibility complex, class I, A (HLA-A),mRNA.
AK301282 - Homo sapiens cDNA FLJ52283 complete cds, highly similar to HLA class I histocompatibility antigen, A-3 alpha chain precursor.
AK301019 - Homo sapiens cDNA FLJ51110 complete cds, highly similar to HLA class I histocompatibility antigen, A-3 alpha chain precursor.
AK125608 - Homo sapiens cDNA FLJ43620 fis, clone SPLEN2021701, highly similar to HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN PRECURSOR.
AK130153 - Homo sapiens cDNA FLJ26643 fis, clone MPE02307, highly similar to HLA class I histocompatibility antigen, A-26(A-10) alpha chain precursor.
AK316362 - Homo sapiens cDNA, FLJ79261 complete cds, highly similar to HLA class I histocompatibility antigen, A-1alpha chain precursor.
AK304472 - Homo sapiens cDNA FLJ51201 complete cds, highly similar to HLA class I histocompatibility antigen, A-3alpha chain precursor.
AK225789 - Homo sapiens mRNA for HLA class I histocompatibility antigen, A-30 alpha chain precursor variant, clone: FCC131E11.
AK130148 - Homo sapiens cDNA FLJ26638 fis, clone MPE01293, highly similar to HLA class I histocompatibility antigen, A-24(A-9) alpha chain precursor.
AK130165 - Homo sapiens cDNA FLJ26655 fis, clone MPE07206, highly similar to HLA class I histocompatibility antigen, A-2 alpha chain precursor.
AK027084 - Homo sapiens cDNA: FLJ23431 fis, clone HRC11886, highly similar to HUMMHAAA Human MHC class I lymphocyte antigen (HLA-A 2402) mRNA.
M23739 - Human major histocompatibility complex class I (HLA-A29.1) gene, complete cds.
BC008611 - Homo sapiens major histocompatibility complex, class I, A, mRNA (cDNA clone MGC:17191 IMAGE:4157200), complete cds.
D32129 - Homo sapiens HLA-A mRNA for MHC class I antigen, complete cds, HLA-A26, clone:cMIY-1.
BC019236 - Homo sapiens major histocompatibility complex, class I, A, mRNA (cDNA clone MGC:2384 IMAGE:2821717), complete cds.
BC003069 - Homo sapiens major histocompatibility complex, class I, A, mRNA (cDNA clone MGC:2166 IMAGE:3510139), complete cds.
AJ002678 - Homo sapiens HLA-A gene, exons 1 2 and 3, A*7403.
AJ223060 - Homo sapiens HLA-A*7402 gene, exons 1-3.
X95409 - Homo sapiens HLA-A gene (allele A*7402).
X95561 - Homo sapiens HLA-A gene (allele A*74pb).
Y13267 - Homo sapiens mRNA for human leukocyte antigen, HLA-A2 variant.
CU676396 - Synthetic construct Homo sapiens gateway clone IMAGE:100017110 5' read HLA-A mRNA.
U17571 - Human isolate GU5175 MHC class I HLA-A-6601 mRNA, partial cds.
AF015930 - Homo sapiens MHC class I antigen HLA-A (HLA-A) mRNA, partial cds.
AY225407 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*3303 allele, partial cds.
AB590186 - Synthetic construct DNA, clone: pFN21AE1575, Homo sapiens HLA-A gene for major histocompatibility complex, class I, A, without stop codon, in Flexi system.
DQ891760 - Synthetic construct clone IMAGE:100004390; FLH179684.01X; RZPDo839B05132D major histocompatibility complex, class I, A (HLA-A) gene, encodes complete protein.
EU176622 - Synthetic construct Homo sapiens clone IMAGE:100011430; FLH179683.01L; RZPDo839B07254D major histocompatibility complex, class I, A (HLA-A) gene, encodes complete protein.
X60108 - H.sapiens gene for HLA-A2902.
AF036921 - Homo sapiens MHC class I antigen HLA-A mRNA (HLA-A*0201 variant allele), complete cds.
AF116214 - Homo sapiens MHC class I antigen heavy chain HLA-A mRNA (HLA-A*2422 allele), complete cds.
AF116215 - Homo sapiens MHC class I antigen heavy chain HLA-A mRNA (HLA-A*0230 allele), complete cds.
AF140506 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*0233 allele, complete cds.
AF165065 - Homo sapiens HLA class I antigen (HLA-A) mRNA, HLA-A*1101 variant allele, complete cds.
AF217560 - Homo sapiens MHC class I antigen heavy chain (HLA-A) mRNA, HLA-A*3205 allele, complete cds.
AF217561 - Homo sapiens MHC class I antigen heavy chain (HLA-A) mRNA, HLA-A*0302 allele, complete cds.
AF287958 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A32 allele, complete cds, alternatively spliced.
AF287959 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A32L allele, complete cds, alternatively spliced.
AJ000661 - Homo sapiens mRNA for HLA-A*2903 allele.
AJ249241 - Homo sapiens mRNA for MHC class 1 antigen, A*0209 allele.
AY365426 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*0201 allele, complete cds.
AY786585 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*11new allele, complete cds, alternatively spliced.
AY786588 - Homo sapiens nonfunctional MHC class I antigen (HLA-A) mRNA, HLA-A*11new allele, complete sequence, alternatively spliced.
AY787587 - Homo sapiens nonfunctional MHC class I antigen (HLA-A) mRNA, HLA-A*11new allele, complete sequence, alternatively spliced.
AY856830 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*020604 allele, complete cds.
D14350 - Homo sapiens mRNA for HLA-A26.1 antigen, complete cds.
D14351 - Homo sapiens mRNA for HLA-A26.4 antigen, complete cds.
D14354 - Homo sapiens mRNA for HLA-A10SA antigen, complete cds.
D16841 - Homo sapiens A1101 mRNA for HLA-A11 antigen A11.1, complete cds.
D16842 - Homo sapiens A1102 mRNA for HLA-A11 antigen A11.2, complete cds.
D16843 - Homo sapiens mRNA for HLA-A26.3 antigen, complete cds.
D26550 - Homo sapiens HLA-A24AK mRNA, complete cds.
D38525 - Homo sapiens HLA-A mRNA, complete cds, HLA-A null allele HLA-A*0215N.
D50068 - Homo sapiens mRNA for HLA-A26, complete cds.
D83515 - Homo sapiens mRNA for HLA-A*0218, complete cds.
D83516 - Homo sapiens mRNA for HLA-A9HH antigen, complete cds.
DQ327718 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*310102 allele, complete cds.
DQ327719 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*330301 allele, complete cds.
DQ327720 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*260101 allele, complete cds.
DQ327721 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*110101 allele, complete cds.
DQ327722 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*24020101 allele, complete cds.
DQ336693 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*020301 allele, complete cds.
DQ336695 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*300101 allele, complete cds.
FM202434 - Homo sapiens mRNA for MHC class I antigen (HLA-A gene), HLA-A*24new allele.
L06425 - Human MHC class II HLA-A (HLA A-68012) mRNA, exons 1-6.
L06440 - Human lymphocyte antigen A33 mRNA, complete cds.
M24042 - Human MHC class I HLA-A2.4a chain mRNA (A2.4a, B46, Cw11), complete cds.
M32321 - Human MHC HLA protein, allele A25, complete cds.
M64740 - Homo sapiens MHC class I antigen (HLA-A) mRNA, complete cds.
M84375 - Homo sapiens MHC class I antigen (HLA) mRNA, HLA-A*3101 allele, complete cds.
M84377 - Human MHC class I lymphocyte antigen (HLA-A*0211) mRNA, complete cds.
M84378 - Human MHC class I lymphocyte antigen (HLA-A*0212) mRNA, complete cds.
M84379 - Homo sapiens MHC class I lymphocyte antigen (HLA-A) mRNA, complete cds.
M98453 - Homo sapiens MHC HLA-A cell surface glycoprotein (HLA-A) mRNA, HLA-A*2602 allele, complete cds.
U03697 - Human HLA A-2601 mRNA, complete cds.
U03907 - Human MHC Class I HLA-B-3201 mRNA, complete cds.
U07161 - Human MHC class I HLA-A (HLA-A-0102 allele) mRNA, complete cds.
U07234 - Human MHC class I HLA-A19 (HLA-A-3004 allele) mRNA, complete cds.
U17569 - Human isolate GU2037 MHC class I HLA-A-7401 mRNA, complete cds.
U17570 - Human isolate GU2040 MHC class I HLA-A-7401 mRNA, complete cds.
U18930 - Human MHC class I antigen HLA-A2 (HLA-A2) mRNA, complete cds.
U24261 - Human MHC class I antigen HLA-A30 (HLA-A-3004 allele) mRNA, complete cds.
U32184 - Human MHC class I HLA-A (HLA-A-0302-new allele) mRNA, complete cds.
U41057 - Human HLA class I A locus antigen A*68new mRNA, complete cds.
U45480 - Human HLA class I A mRNA, allele A*2601new, complete cds.
U50574 - Human MHC class I HLA-A allele (HLA-A) mRNA, complete cds.
U52429 - Human cell surface glycoprotein (HLA-A26) mRNA, complete cds.
U56825 - Human MHC class I antigen HLA-A2 mRNA, complete cds.
U83415 - Human MHC class I antigen HLA-A (HLA-A*2901 allele) mRNA, complete cds.
U83416 - Human MHC class I antigen HLA-A (HLA-A*3301 allele) mRNA, complete cds.
X61700 - Human RNA for HLA-Aw36 antigen.
X61701 - Human RNA for HLA-Aw74 antigen.
X61702 - Human RNA for HLA-A30.2 antigen.
X61703 - Human RNA for HLA-Aw43 antigen.
X61704 - Human RNA for HLA-Aw34.1 antigen.
X61705 - Human RNA for HLA-Aw34.2 antigen.
X61711 - Human RNA for HLA-Aw661 antigen.
X61712 - Human RNA for HLA-A*6602 antigen.
X96724 - Homo sapiens mRNA for human leukocyte antigen HLA-A-02.
X97120 - H.sapiens mRNA for HLA-A-32 allele.
X97802 - H.sapiens mRNA for human leucocyte antigen, HLA-A25.
Y11441 - H.sapiens mRNA for MHC class I human leukocyte antigen, allele HLA-A*02.
Z23071 - H.sapiens mRNA for HLA-A*0210.
Z27120 - H.sapiens mRNA for HLA-A2 SLU.
Z46633 - H.sapiens hla-A gene for lymphocyte antigen.
U03754 - Homo sapiens MHC class I antigen HLA-A (HLA-A) mRNA, complete cds.
U09740 - Human MHC class I antigen HLA-A33 (HLA-A*3303) mRNA, complete cds.
X51745 - Human mRNA for LA45 gene.
X13111 - Human mRNA for HLA-A11E, a MHC class I molecule (major histocompatibility complex).
AB209117 - Homo sapiens mRNA for HLA class I histocompatibility antigen, A-1 alpha chain precursor variant protein.
AF305699 - Homo sapiens MHC class I antigen precursor (HLA-A) mRNA, HLA-A*0214 allele, partial cds.
L19403 - Human MHC HLA allele A*8001 mRNA sequence.
AF008933 - Homo sapiens MHC class I antigen HLA-A heavy chain (HLA-A*0226) mRNA, partial cds.
M94880 - Human MHC class I (HLA-A*8001) mRNA.
M86404 - Human MHC class I (HLA-A 0204) mRNA fragment.
X57954 - H.sapiens mRNA for HLA-A*0204.
X60764 - H.sapiens mRNA HLA-A2.5 antigen.
AY191309 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*0201 allele, partial cds.
AY191310 - Homo sapiens MHC class I antigen (HLA-A) mRNA, HLA-A*0207 allele, partial cds.
AF012767 - Homo sapiens MHC class I antigen HLA-A heavy chain (allele A*3301) mRNA, partial cds.
AJ001274 - Homo sapiens HLA-A68 gene, exons 2 and 3.
U43335 - Human MHC class I antigen HLA-A mRNA, partial cds.
U43336 - Human MHC class I antigen HLA-A mRNA, partial cds.
X91399 - H.sapiens mRNA for HLA-A11 antigen.
X96638 - Homo sapiens HLA-A gene, A66Ka exon2 2 and 3.
Y08275 - Homo sapiens HLA-A11 gene, exon 2 and exon 3.
AJ290394 - Homo sapiens partial mRNA for MHC class I antigen (HLA-A gene), HLA-A*26 allele.
AJ580771 - Homo sapiens partial mRNA for MHC class I antigen (HLA-A gene), HLA-A*26 allele.
X94568 - Homo sapiens HLA-A*0204 gene exons 2 & 3.
M24095 - Human MHC class I HLA-A10-alpha-2 chain mRNA, partial cds, clone 8/16.
X02457 - Human mRNA fragment for HLA-A2 class I antigen.
M11887 - Human MHC class I HLA-A allele HLA-10, 3' end.
M27539 - Human MHC class I HLA-A cell surface antigen mRNA, (HLA-A28,-B40, -Cw3), clone LB45.
M12377 - Human MHC class I HLA-A24 glycoprotein mRNA, 3' end.
DQ600446 - Homo sapiens piRNA piR-38512, complete sequence.
DQ580344 - Homo sapiens piRNA piR-48456, complete sequence.
HG327114 - Homo sapiens mRNA for MHC class I antigen (HLA-A gene), isolate 3943, allele HLA-A.
HG327116 - Homo sapiens mRNA for MHC class I antigen (HLA-A gene), isolate 8072, allele HLA-A*01:37.
HG327118 - Homo sapiens mRNA for MHC class I antigen (HLA-A gene), isolate 17772, allele HLA-A*02:17:02.
AB910260 - Homo sapiens HLA-A mRNA for MHC class I antigen, partial cds, allele: HLA-A*32:01:01.

-  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

BioCarta from NCI Cancer Genome Anatomy Project
h_nkcellsPathway - Ras-Independent pathway in NK cell-mediated cytotoxicity
h_ctlPathway - CTL mediated immune response against target cells
h_mhcPathway - Antigen Processing and Presentation

-  Other Names for This Gene
  Alternate Gene Symbols: AF287958, B0UXQ1, B0UXQ1_HUMAN, DAMA-247D1.1-003, uc011gqv.2
UCSC ID: uc011gqw.2
RefSeq Accession: NM_002116

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AF287958.1
exon count: 6CDS single in 3' UTR: no RNA size: 981
ORF size: 975CDS single in intron: no Alignment % ID: 98.27
txCdsPredict score: 1125.00frame shift in genome: no % Coverage: 99.49
has start codon: yes stop codon in genome: no # of Alignments: 8
has end codon: no 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.