LOCUS       NM_020056               1458 bp    mRNA    linear   PRI 07-FEB-2025
DEFINITION  Homo sapiens major histocompatibility complex, class II, DQ alpha 2
            (HLA-DQA2), mRNA.
ACCESSION   NM_020056 XM_005249050 XM_005272806 XM_005274854 XM_005275110
            XM_005275385 XM_005275545
VERSION     NM_020056.5
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 1458)
  AUTHORS   Chen,L., Zhao,Y., Li,M. and Lv,G.
  TITLE     Proteome-wide Mendelian randomization highlights AIF1 and HLA-DQA2
            as targets for primary sclerosing cholangitis
  JOURNAL   Hepatol Int 18 (2), 517-528 (2024)
   PUBMED   37950809
  REMARK    GeneRIF: Proteome-wide Mendelian randomization highlights AIF1 and
            HLA-DQA2 as targets for primary sclerosing cholangitis.
REFERENCE   2  (bases 1 to 1458)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   3  (bases 1 to 1458)
  AUTHORS   Liang,S.Q., Deng,J.M., Wei,X., Chen,Z.R., Yang,M.L., Qin,H.J.,
            Zhang,J.Q. and He,Z.Y.
  TITLE     Association of GWAS-supported noncoding area loci rs404860,
            rs3117098, and rs7775228 with asthma in Chinese Zhuang population
  JOURNAL   J Clin Lab Anal 34 (2), e23066 (2020)
   PUBMED   31605414
  REMARK    GeneRIF: Association of GWAS-supported noncoding area loci
            rs404860, rs3117098, and rs7775228 with asthma in Chinese Zhuang
            population.
REFERENCE   4  (bases 1 to 1458)
  AUTHORS   Armstrong,D.L., Zidovetzki,R., Alarcon-Riquelme,M.E., Tsao,B.P.,
            Criswell,L.A., Kimberly,R.P., Harley,J.B., Sivils,K.L., Vyse,T.J.,
            Gaffney,P.M., Langefeld,C.D. and Jacob,C.O.
  TITLE     GWAS identifies novel SLE susceptibility genes and explains the
            association of the HLA region
  JOURNAL   Genes Immun 15 (6), 347-354 (2014)
   PUBMED   24871463
REFERENCE   5  (bases 1 to 1458)
  AUTHORS   Chang,S.W., Fann,C.S., Su,W.H., Wang,Y.C., Weng,C.C., Yu,C.J.,
            Hsu,C.L., Hsieh,A.R., Chien,R.N., Chu,C.M. and Tai,D.I.
  TITLE     A genome-wide association study on chronic HBV infection and its
            clinical progression in male Han-Taiwanese
  JOURNAL   PLoS One 9 (6), e99724 (2014)
   PUBMED   24940741
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1458)
  AUTHORS   Marsh,S.G. and Bodmer,J.G.
  TITLE     HLA class II nucleotide sequences, 1992
  JOURNAL   Tissue Antigens 40 (5), 229-243 (1992)
   PUBMED   1362295
  REMARK    Correction to:[Tissue Antigens. 1992 Apr;39(4):161-73. doi:
            10.1111/j.1399-0039.1992.tb01932.x.. PMID: 1529427]
REFERENCE   7  (bases 1 to 1458)
  AUTHORS   Wang,Y., Lu,P., Zhou,K., Clay,T., Wood,N., Bradley,B. and
            Bidwell,J.
  TITLE     Nucleotide sequencing of HLA-DQ gene second exons in Chinese
            homozygous cells
  JOURNAL   Eur J Immunogenet 19 (5), 287-293 (1992)
   PUBMED   1420115
REFERENCE   8  (bases 1 to 1458)
  AUTHORS   Kenter,M., Otting,N., Anholts,J., Leunissen,J., Jonker,M. and
            Bontrop,R.E.
  TITLE     Evolutionary relationships among the primate Mhc-DQA1 and DQA2
            alleles
  JOURNAL   Immunogenetics 36 (2), 71-78 (1992)
   PUBMED   1612647
REFERENCE   9  (bases 1 to 1458)
  AUTHORS   Gyllensten,U.B. and Erlich,H.A.
  TITLE     Ancient roots for polymorphism at the HLA-DQ alpha locus in
            primates
  JOURNAL   Proc Natl Acad Sci U S A 86 (24), 9986-9990 (1989)
   PUBMED   2513578
REFERENCE   10 (bases 1 to 1458)
  AUTHORS   Jonsson,A.K., Hyldig-Nielsen,J.J., Servenius,B., Larhammar,D.,
            Andersson,G., Jorgensen,F., Peterson,P.A. and Rask,L.
  TITLE     Class II genes of the human major histocompatibility complex.
            Comparisons of the DQ and DX alpha and beta genes
  JOURNAL   J Biol Chem 262 (18), 8767-8777 (1987)
   PUBMED   3036828
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL672104.4.
            
            On May 17, 2019 this sequence version replaced NM_020056.4.
            
            Summary: This gene belongs to the HLA class II alpha chain family.
            The encoded protein forms a heterodimer with a class II beta chain.
            It is located in intracellular vesicles and plays a central role in
            the peptide loading of MHC class II molecules by helping to release
            the CLIP molecule from the peptide binding site. Class II molecules
            are expressed in antigen presenting cells (B lymphocytes, dendritic
            cells, macrophages) and are used to present antigenic peptides on
            the cell surface to be recognized by CD4 T-cells. [provided by
            RefSeq, Jun 2010].
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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##
            RNAseq introns :: single sample supports all introns SAMEA2144335,
                              SAMEA2145893 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000374940.4/ ENSP00000364076.3
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-135               AL672104.4         5734-5868
            136-384             AL672104.4         9502-9750
            385-666             AL672104.4         10134-10415
            667-841             AL672104.4         10583-10757
            842-1458            AL672104.4         10925-11541
FEATURES             Location/Qualifiers
     source          1..1458
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p21.32"
     gene            1..1458
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /note="major histocompatibility complex, class II, DQ
                     alpha 2"
                     /db_xref="GeneID:3118"
                     /db_xref="HGNC:HGNC:4943"
                     /db_xref="MIM:613503"
     exon            1..135
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /inference="alignment:Splign:2.1.0"
     CDS             54..821
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /note="HLA class II histocompatibility antigen, DQ alpha 2
                     chain; MHC class II DQA2; DX alpha chain; HLA class II
                     histocompatibility antigen, DQ(6) alpha chain; MHC class
                     II antigen; MHC class II DQA1; HLA class II
                     histocompatibility antigen, DQ alpha 1 chain; DC-1 alpha
                     chain; MHC class I antigen"
                     /codon_start=1
                     /product="HLA class II histocompatibility antigen, DQ
                     alpha 2 chain precursor"
                     /protein_id="NP_064440.1"
                     /db_xref="CCDS:CCDS4753.1"
                     /db_xref="GeneID:3118"
                     /db_xref="HGNC:HGNC:4943"
                     /db_xref="MIM:613503"
                     /translation="MILNKALLLGALALTAVMSPCGGEDIVADHVASYGVNFYQSHGP
                     SGQYTHEFDGDEEFYVDLETKETVWQLPMFSKFISFDPQSALRNMAVGKHTLEFMMRQ
                     SNSTAATNEVPEVTVFSKFPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSE
                     TSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTET
                     LVCALGLSVGLMGIVVGTVFIIQGLRSVGASRHQGLL"
     exon            136..384
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /inference="alignment:Splign:2.1.0"
     exon            385..666
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /inference="alignment:Splign:2.1.0"
     exon            667..841
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /inference="alignment:Splign:2.1.0"
     exon            842..1458
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1134..1139
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /note="hexamer: AATAAA"
     polyA_site      1158
                     /gene="HLA-DQA2"
                     /gene_synonym="DC-alpha; DQA1; DX-ALPHA; HLA-DCA; HLA-DXA;
                     HLADQA2"
                     /note="major polyA site"
ORIGIN      
        1 acaattgctc tacagctcag agcagcaact gctgaggctg ccttgggaag aagatgatcc
       61 taaacaaagc tctgctgctg ggggccctcg ccctgactgc cgtgatgagc ccctgtggag
      121 gtgaagacat tgtggctgac catgttgcct cctatggtgt gaacttctac cagtctcacg
      181 gtccctctgg ccagtacacc catgaatttg atggagacga ggagttctat gtggacctgg
      241 agacgaaaga gactgtctgg cagttgccta tgtttagcaa atttataagt tttgacccgc
      301 agagtgcact gagaaatatg gctgtgggaa aacacacctt ggaattcatg atgagacagt
      361 ccaactctac cgctgccacc aatgaggttc ctgaggtcac agtgttttcc aagtttcctg
      421 tgacgctggg tcagcccaac accctcatct gtcttgtgga caacatcttt cctcctgtgg
      481 tcaacatcac ctggctgagc aatgggcact cagtcacaga aggtgtttct gagaccagct
      541 tcctctccaa gagtgatcat tccttcttca agatcagtta cctcaccttc ctcccttctg
      601 ctgatgagat ttatgactgc aaggtggagc actggggcct ggacgagcct cttctgaaac
      661 actgggagcc tgagattcca gcccctatgt cagagctcac agagactttg gtctgcgccc
      721 tggggttgtc tgtgggcctc atgggcattg tggtgggcac tgtcttcatc atccaaggcc
      781 tgcgttcagt tggtgcttcc agacaccaag ggctcttatg aatcccatcc tgaaaaggaa
      841 ggtgcatcac catctacagg agaagaagaa tggacttgct aaatgaccta gcactattct
      901 ctggcctgat ttatcatatc ccttttctcc tccaaatgtt tcttctctca cctcttctct
      961 gggacttaag gtgctatatt ccctcagagc tcacaaatgc ctttcaattc tttccctgac
     1021 ctcctttcct gaattttttt attttctcaa atgttaccta ctaagggatg cctgggtaag
     1081 ccactcagct acctaattcc tcaatgacct ttatctaaaa tctccatgga agcaataaat
     1141 tcccttttga tgcctctatt gaatttttcc catctttcat ctcagggctg actgagagca
     1201 taacttagaa tgggcgactc ttatgtttta ggccaatttc atatcattcc ccagatcata
     1261 tttcaagtcc agtaacacag gagcaaccaa gtacagtgta tcctgataat ttgttgattt
     1321 cttaactggt gttaatattt ctttcttcct tttgttccta cccttggcca ctgccagcca
     1381 cccctcaatt caggtaccaa cgaaccctct gcccttggct cagaatggtt atagcagaaa
     1441 tacaaaaaaa aaaaaaaa
//
