LOCUS       NM_002117               1542 bp    mRNA    linear   PRI 15-OCT-2024
DEFINITION  Homo sapiens major histocompatibility complex, class I, C (HLA-C),
            transcript variant 1, mRNA.
ACCESSION   NM_002117 XM_001131707
VERSION     NM_002117.6
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 1542)
  AUTHORS   Ciolfi,C., Sernicola,A. and Alaibac,M.
  TITLE     HLA-Cw6 Polymorphism in Autoimmune Blistering Diseases
  JOURNAL   Biomolecules 14 (9), 1150 (2024)
   PUBMED   39334916
  REMARK    GeneRIF: HLA-Cw6 Polymorphism in Autoimmune Blistering Diseases.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1542)
  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 1542)
  AUTHORS   Mikaeeli,S., Ben Djoudi Ouadda,A., Evagelidis,A., Essalmani,R.,
            Ramos,O.H.P., Fruchart-Gaillard,C. and Seidah,N.G.
  TITLE     Insights into PCSK9-LDLR Regulation and Trafficking via the
            Differential Functions of MHC-I Proteins HFE and HLA-C
  JOURNAL   Cells 13 (10), 857 (2024)
   PUBMED   38786080
  REMARK    GeneRIF: Insights into PCSK9-LDLR Regulation and Trafficking via
            the Differential Functions of MHC-I Proteins HFE and HLA-C.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1542)
  AUTHORS   Naidoo,L., Arumugam,T. and Ramsuran,V.
  TITLE     HLA-B and C Expression Contributes to COVID-19 Disease Severity
            within a South African Cohort
  JOURNAL   Genes (Basel) 15 (4), 522 (2024)
   PUBMED   38674456
  REMARK    GeneRIF: HLA-B and C Expression Contributes to COVID-19 Disease
            Severity within a South African Cohort.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1542)
  AUTHORS   Altalhi,R.A., Aljuaimlani,A., Alswayyed,M., Arafah,M.,
            Tashkandy,Y., Almutairi,B.O., Mansour,L. and Alomar,S.Y.
  TITLE     Association of the Genetic Diversity of Killer Cell
            Immunoglobulin-like Receptor Genes and HLA-C Ligand in Saudi Women
            With Thyroid Cancer
  JOURNAL   Cancer Control 31, 10732748241274495 (2024)
   PUBMED   39365900
  REMARK    GeneRIF: Association of the Genetic Diversity of Killer Cell
            Immunoglobulin-like Receptor Genes and HLA-C Ligand in Saudi Women
            With Thyroid Cancer.
REFERENCE   6  (bases 1 to 1542)
  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 1542)
  AUTHORS   Zemmour,J. and Parham,P.
  TITLE     Distinctive polymorphism at the HLA-C locus: implications for the
            expression of HLA-C
  JOURNAL   J Exp Med 176 (4), 937-950 (1992)
   PUBMED   1383381
REFERENCE   8  (bases 1 to 1542)
  AUTHORS   Belich,M.P., Madrigal,J.A., Hildebrand,W.H., Zemmour,J.,
            Williams,R.C., Luz,R., Petzl-Erler,M.L. and Parham,P.
  TITLE     Unusual HLA-B alleles in two tribes of Brazilian Indians
  JOURNAL   Nature 357 (6376), 326-329 (1992)
   PUBMED   1317015
REFERENCE   9  (bases 1 to 1542)
  AUTHORS   Zemmour,J., Gumperz,J.E., Hildebrand,W.H., Ward,F.E., Marsh,S.G.,
            Williams,R.C. and Parham,P.
  TITLE     The molecular basis for reactivity of anti-Cw1 and anti-Cw3
            alloantisera with HLA-B46 haplotypes
  JOURNAL   Tissue Antigens 39 (5), 249-257 (1992)
   PUBMED   1384166
REFERENCE   10 (bases 1 to 1542)
  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 AL671883.3 and BC007814.2.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_002117.5.
            
            Summary: HLA-C 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 endoplasmic
            reticulum lumen. They are expressed in nearly all cells. The heavy
            chain is approximately 45 kDa and its gene contains 8 exons. Exon
            one encodes the leader peptide, exons 2 and 3 encode the alpha1 and
            alpha2 domain, 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. About 6000 HLA-C
            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 C*07:02:01
            allele of the HLA-C gene, as represented in the assembled
            chromosome 6 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 :: BC033293.1, M26429.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2144333, SAMEA2149398
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            coronavirus related    :: involved in immune response or antiviral
                                      activity
            MANE Ensembl match     :: ENST00000376228.10/ ENSP00000365402.5
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-23                AL671883.3         7266-7288           c
            24-1539             BC007814.2         1-1516
            1540-1542           AL671883.3         3945-3947           c
FEATURES             Location/Qualifiers
     source          1..1542
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p21.33"
     gene            1..1542
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /note="major histocompatibility complex, class I, C"
                     /db_xref="GeneID:3107"
                     /db_xref="HGNC:HGNC:4933"
                     /db_xref="MIM:142840"
     exon            1..94
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /inference="alignment:Splign:2.1.0"
     CDS             22..1122
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /note="HLA class I histocompatibility antigen, C alpha
                     chain; MHC class I antigen heavy chain HLA-C; major
                     histocompatibility antigen HLA-C; human leukocyte
                     antigen-C alpha chain; HLA-C antigen"
                     /codon_start=1
                     /product="HLA class I histocompatibility antigen, C alpha
                     chain precursor"
                     /protein_id="NP_002108.4"
                     /db_xref="CCDS:CCDS34393.1"
                     /db_xref="GeneID:3107"
                     /db_xref="HGNC:HGNC:4933"
                     /db_xref="MIM:142840"
                     /translation="MRVMAPRALLLLLSGGLALTETWACSHSMRYFDTAVSRPGRGEP
                     RFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQADRVSL
                     RNLRGYYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKDYIALNEDLRSWTAA
                     DTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRAEPPKTHVTHHPL
                     SDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSG
                     QEQRYTCHMQHEGLQEPLTLSWEPSSQPTIPIMGIVAGLAVLVVLAVLGAVVTAMMCR
                     RKSSGGKGGSCSQAACSNSAQGSDESLITCKA"
     exon            95..364
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /inference="alignment:Splign:2.1.0"
     exon            365..640
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /inference="alignment:Splign:2.1.0"
     exon            641..916
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /inference="alignment:Splign:2.1.0"
     exon            917..1036
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /inference="alignment:Splign:2.1.0"
     exon            1037..1069
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /inference="alignment:Splign:2.1.0"
     exon            1070..1117
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /inference="alignment:Splign:2.1.0"
     exon            1118..1542
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1517..1522
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /note="hexamer: AATAAA"
     polyA_site      1542
                     /gene="HLA-C"
                     /gene_synonym="D6S204; HLA-JY3; HLAC; HLC-C; MHC; PSORS1"
                     /note="major polyA site"
ORIGIN      
        1 acattctccc cagaggccga gatgcgggtc atggcgcccc gagccctcct cctgctgctc
       61 tcgggaggcc tggccctgac cgagacctgg gcctgctccc actccatgag gtatttcgac
      121 accgccgtgt cccggcccgg ccgcggagag ccccgcttca tctcagtggg ctacgtggac
      181 gacacgcagt tcgtgcggtt cgacagcgac gccgcgagtc cgagagggga gccgcgggcg
      241 ccgtgggtgg agcaggaggg gccggagtat tgggaccggg agacacagaa gtacaagcgc
      301 caggcacagg ctgaccgagt gagcctgcgg aacctgcgcg gctactacaa ccagagcgag
      361 gacgggtctc acaccctcca gaggatgtct ggctgcgacc tggggcccga cgggcgcctc
      421 ctccgcgggt atgaccagtc cgcctacgac ggcaaggatt acatcgccct gaacgaggac
      481 ctgcgctcct ggaccgccgc ggacaccgcg gctcagatca cccagcgcaa gttggaggcg
      541 gcccgtgcgg cggagcagct gagagcctac ctggagggca cgtgcgtgga gtggctccgc
      601 agatacctgg agaacgggaa ggagacgctg cagcgcgcag aacccccaaa gacacacgtg
      661 acccaccacc ccctctctga ccatgaggcc accctgaggt gctgggccct gggcttctac
      721 cctgcggaga tcacactgac ctggcagcgg gatggggagg accagaccca ggacaccgag
      781 cttgtggaga ccaggccagc aggagatgga accttccaga agtgggcagc tgtggtggtg
      841 ccttctggac aagagcagag atacacgtgc catatgcagc acgaggggct gcaagagccc
      901 ctcaccctga gctgggagcc atcttcccag cccaccatcc ccatcatggg catcgttgct
      961 ggcctggctg tcctggttgt cctagctgtc cttggagctg tggtcaccgc tatgatgtgt
     1021 aggaggaaga gctcaggtgg aaaaggaggg agctgctctc aggctgcgtg cagcaacagt
     1081 gcccagggct ctgatgagtc tctcatcact tgtaaagcct gagacagctg cctgtgtggg
     1141 actgagatgc aggatttctt cacacctctc ctttgtgact tcaagagcct ctggcatctc
     1201 tttctgcaaa ggcacctgaa tgtgtctgcg ttcctgttag cataatgtga ggaggtggag
     1261 agacagccca cccccgtgtc caccgtgacc cctgtcccca cactgacctg tgttccctcc
     1321 ccgatcatct ttcctgttcc agagaggtgg ggctggatgt ctccatctct gtctcaaatt
     1381 catggtgcac tgagctgcaa cttcttactt ccctaatgaa gttaagaacc tgaatataaa
     1441 tttgtgttct caaatatttg ctatgaagcg ttgatggatt aattaaataa gtcaattcct
     1501 agaagttgag agagcaaata aagacctgag aaccttccag aa
//
