LOCUS       NM_002116               1535 bp    mRNA    linear   PRI 12-NOV-2024
DEFINITION  Homo sapiens major histocompatibility complex, class I, A (HLA-A),
            transcript variant 1 (A*03:01:01:01), mRNA.
ACCESSION   NM_002116 NM_001080840 XM_001713645 XM_005275330 XM_006725858
            XM_006725946 XM_006726136 XM_011548124 XM_017030288
VERSION     NM_002116.8
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1535)
  AUTHORS   de Melo,A.C., Lucena,E., de Oliveira,D.C.M. and Viola,J.P.B.
  TITLE     Frequency of HLA-A*02:01 in the Brazilian population and its impact
            on uveal melanoma systemic treatment
  JOURNAL   Oncologist 29 (8), e1098-e1099 (2024)
   PUBMED   38785402
  REMARK    GeneRIF: Frequency of HLA-A*02:01 in the Brazilian population and
            its impact on uveal melanoma systemic treatment.
REFERENCE   2  (bases 1 to 1535)
  AUTHORS   Wang,T., Wang,M., Qi,J., Li,Y., Wu,J., Shang,L. and Chen,L.
  TITLE     [Genetic study of a rare Chinese pedigree with a recombination
            occurring between the HLA-A/C loci in both parents]
  JOURNAL   Zhonghua Yi Xue Yi Chuan Xue Za Zhi 41 (7), 853-857 (2024)
   PUBMED   38946372
  REMARK    GeneRIF: [Genetic study of a rare Chinese pedigree with a
            recombination occurring between the HLA-A/C loci in both parents].
REFERENCE   3  (bases 1 to 1535)
  AUTHORS   Xu,Z.M., Gnouamozi,G.E., Rueger,S., Shea,P.R., Buti,M., Chan,H.L.,
            Marcellin,P., Lawless,D., Naret,O., Zeller,M., Schneuing,A.,
            Scheck,A., Junier,T., Moradpour,D., Podlaha,O., Suri,V., Gaggar,A.,
            Subramanian,M., Correia,B., Gfeller,D., Urban,S. and Fellay,J.
  TITLE     Joint host-pathogen genomic analysis identifies hepatitis B virus
            mutations associated with human NTCP and HLA class I variation
  JOURNAL   Am J Hum Genet 111 (6), 1018-1034 (2024)
   PUBMED   38749427
  REMARK    GeneRIF: Joint host-pathogen genomic analysis identifies hepatitis
            B virus mutations associated with human NTCP and HLA class I
            variation.
REFERENCE   4  (bases 1 to 1535)
  AUTHORS   Kohansal Vajari,M., Ehsan,M., Ghiasi,S., Fooladi,S., Karami,N.,
            Hassanshahi,G. and Fatemi,A.
  TITLE     Human Leukocyte Antigen Alleles (HLA-A, HLA-B, and HLA-DRB1) are
            associated with Acute Lymphoblastic Leukemia (ALL) : A Case-Control
            Study in a Sample of Iranian Population
  JOURNAL   Asian Pac J Cancer Prev 25 (5), 1507-1513 (2024)
   PUBMED   38809622
  REMARK    GeneRIF: Human Leukocyte Antigen Alleles (HLA-A, HLA-B, and
            HLA-DRB1) are associated with Acute Lymphoblastic Leukemia (ALL) :
            A Case-Control Study in a Sample of Iranian Population.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1535)
  AUTHORS   Yang,K., Chen,G., Yu,F., Fang,X., Zhang,J., Zhang,Z., Shi,Y. and
            Zhang,L.
  TITLE     Molecular mechanism of specific HLA-A mRNA recognition by the
            RNA-binding-protein hMEX3B to promote tumor immune escape
  JOURNAL   Commun Biol 7 (1), 158 (2024)
   PUBMED   38326406
  REMARK    GeneRIF: Molecular mechanism of specific HLA-A mRNA recognition by
            the RNA-binding-protein hMEX3B to promote tumor immune escape.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1535)
  AUTHORS   Nguyen,A., David,J.K., Maden,S.K., Wood,M.A., Weeder,B.R.,
            Nellore,A. and Thompson,R.F.
  TITLE     Human Leukocyte Antigen Susceptibility Map for Severe Acute
            Respiratory Syndrome Coronavirus 2
  JOURNAL   J Virol 94 (13), e00510-20 (2020)
   PUBMED   32303592
  REMARK    Publication Status: Online-Only
REFERENCE   7  (bases 1 to 1535)
  AUTHORS   Krangel,M.S., Orr,H.T. and Strominger,J.L.
  TITLE     Assembly and maturation of HLA-A and HLA-B antigens in vivo
  JOURNAL   Cell 18 (4), 979-991 (1979)
   PUBMED   93026
REFERENCE   8  (bases 1 to 1535)
  AUTHORS   Orr,H.T., Lopez de Castro,J.A., Parham,P., Ploegh,H.L. and
            Strominger,J.L.
  TITLE     Comparison of amino acid sequences of two human histocompatibility
            antigens, HLA-A2 and HLA-B7: location of putative alloantigenic
            sites
  JOURNAL   Proc Natl Acad Sci U S A 76 (9), 4395-4399 (1979)
   PUBMED   92029
REFERENCE   9  (bases 1 to 1535)
  AUTHORS   Parham,P., Alpert,B.N., Orr,H.T. and Strominger,J.L.
  TITLE     Carbohydrate moiety of HLA antigens. Antigenic properties and amino
            acid sequences around the site of glycosylation
  JOURNAL   J Biol Chem 252 (21), 7555-7567 (1977)
   PUBMED   72068
REFERENCE   10 (bases 1 to 1535)
  AUTHORS   Peterson,P.A., Rask,L., Sege,K., Klareskog,L., Anundi,H. and
            Ostberg,L.
  TITLE     Evolutionary relationship between immunoglobulins and
            transplantation antigens
  JOURNAL   Proc Natl Acad Sci U S A 72 (4), 1612-1616 (1975)
   PUBMED   1055432
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK313119.1, U32184.1 and
            BE875389.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On or before Nov 22, 2018 this sequence version replaced
            XM_017030288.1, NM_002116.7.
            
            Summary: 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 so that they can be recognized by
            cytotoxic T cells. 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. More than 6000
            HLA-A alleles have been described. The HLA system plays an
            important role in the occurrence and outcome of infectious
            diseases, including those caused by the malaria parasite, the human
            immunodeficiency virus (HIV), and the severe acute respiratory
            syndrome coronavirus (SARS-CoV). The structural spike and the
            nucleocapsid proteins of the novel coronavirus SARS-CoV-2, which
            causes coronavirus disease 2019 (COVID-19), are reported to contain
            multiple Class I epitopes with predicted HLA restrictions.
            Individual HLA genetic variation may help explain different immune
            responses to a virus across a population.[provided by RefSeq, Aug
            2020].
            
            Transcript Variant: This variant (1) represents the A*03:01:0:01
            allele of the HLA-A gene, as found in the primary assembly of the
            reference genome.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR3476690.319220.1,
                                           SRR3476690.280596.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968189
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            coronavirus related    :: involved in immune response or antiviral
                                      activity
            MANE Ensembl match     :: ENST00000376809.10/ ENSP00000366005.5
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-947               AK313119.1         1-947
            948-1110            U32184.1           926-1088
            1111-1535           BE875389.1         86-510
FEATURES             Location/Qualifiers
     source          1..1535
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p22.1"
     gene            1..1535
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /note="major histocompatibility complex, class I, A"
                     /db_xref="GeneID:3105"
                     /db_xref="HGNC:HGNC:4931"
                     /db_xref="MIM:142800"
     exon            1..95
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /inference="alignment:Splign:2.1.0"
     CDS             23..1120
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /note="isoform A*03:01:01:01 precursor is encoded by
                     transcript variant 1 (A*03:01:01:01); HLA class I
                     histocompatibility antigen, A-1 alpha chain; MHC class I
                     antigen HLA-A heavy chain; leukocyte antigen class I-A"
                     /codon_start=1
                     /product="HLA class I histocompatibility antigen, A alpha
                     chain isoform A*03:01:01:01 precursor"
                     /protein_id="NP_002107.3"
                     /db_xref="CCDS:CCDS34373.1"
                     /db_xref="GeneID:3105"
                     /db_xref="HGNC:HGNC:4931"
                     /db_xref="MIM:142800"
                     /translation="MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEP
                     RFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDL
                     GTLRGYYNQSEAGSHTIQIMYGCDVGSDGRFLRGYRQDAYDGKDYIALNEDLRSWTAA
                     DMAAQITKRKWEAAHEAEQLRAYLDGTCVEWLRRYLENGKETLQRTDPPKTHMTHHPI
                     SDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSG
                     EEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRR
                     KSSDRKGGSYTQAASSDSAQGSDVSLTACKV"
     exon            96..365
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /inference="alignment:Splign:2.1.0"
     exon            366..641
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /inference="alignment:Splign:2.1.0"
     exon            642..917
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /inference="alignment:Splign:2.1.0"
     exon            918..1034
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /inference="alignment:Splign:2.1.0"
     exon            1035..1067
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /inference="alignment:Splign:2.1.0"
     exon            1068..1115
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /inference="alignment:Splign:2.1.0"
     exon            1116..1535
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1414..1419
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /note="hexamer: ATTAAA"
     polyA_site      1438
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /note="major polyA site"
     regulatory      1515..1520
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
                     /note="hexamer: AATAAA"
     polyA_site      1535
                     /gene="HLA-A"
                     /gene_synonym="HLAA"
ORIGIN      
        1 agattctccc cagacgccga ggatggccgt catggcgccc cgaaccctcc tcctgctact
       61 ctcgggggcc ctggccctga cccagacctg ggcgggctcc cactccatga ggtatttctt
      121 cacatccgtg tcccggcccg gccgcgggga gccccgcttc atcgccgtgg gctacgtgga
      181 cgacacgcag ttcgtgcggt tcgacagcga cgccgcgagc cagaggatgg agccgcgggc
      241 gccgtggata gagcaggagg ggccggagta ttgggaccag gagacacgga atgtgaaggc
      301 ccagtcacag actgaccgag tggacctggg gaccctgcgc ggctactaca accagagcga
      361 ggccggttct cacaccatcc agataatgta tggctgcgac gtggggtcgg acgggcgctt
      421 cctccgcggg taccggcagg acgcctacga cggcaaggat tacatcgccc tgaacgagga
      481 cctgcgctct tggaccgcgg cggacatggc ggctcagatc accaagcgca agtgggaggc
      541 ggcccatgag gcggagcagt tgagagccta cctggatggc acgtgcgtgg agtggctccg
      601 cagatacctg gagaacggga aggagacgct gcagcgcacg gaccccccca agacacatat
      661 gacccaccac cccatctctg accatgaggc caccctgagg tgctgggccc tgggcttcta
      721 ccctgcggag atcacactga cctggcagcg ggatggggag gaccagaccc aggacacgga
      781 gctcgtggag accaggcctg caggggatgg aaccttccag aagtgggcgg ctgtggtggt
      841 gccttctgga gaggagcaga gatacacctg ccatgtgcag catgagggtc tgcccaagcc
      901 cctcaccctg agatgggagc tgtcttccca gcccaccatc cccatcgtgg gcatcattgc
      961 tggcctggtt ctccttggag ctgtgatcac tggagctgtg gtcgctgccg tgatgtggag
     1021 gaggaagagc tcagatagaa aaggagggag ttacactcag gctgcaagca gtgacagtgc
     1081 ccagggctct gatgtgtccc tcacagcttg taaagtgtga gacagctgcc ttgtgtggga
     1141 ctgagaggca agagttgttc ctgcccttcc ctttgtgact tgaagaaccc tgactttgtt
     1201 tctgcaaagg cacctgcatg tgtctgtgtt cgtgtaggca taatgtgagg aggtggggag
     1261 accaccccac ccccatgtcc accatgaccc tcttcccacg ctgacctgtg ctccctcccc
     1321 aatcatcttt cctgttccag agaggtgggg ctgaggtgtc tccatctctg tctcaacttc
     1381 atggtgcact gagctgtaac ttcttccttc cctattaaaa ttagaacctt agtataaatt
     1441 tactttctca aattcttgcc atgagaggtt gatgagttaa ttaaaggaga agattcctaa
     1501 aatttgagag acaaaataaa tggaagacat gagaa
//
