LOCUS       NM_001008847            1212 bp    mRNA    linear   ROD 22-MAR-2023
DEFINITION  Rattus norvegicus RT1 class II, locus Da (RT1-Da), mRNA.
ACCESSION   NM_001008847 XM_215331
VERSION     NM_001008847.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 1212)
  AUTHORS   Tuncel J, Haag S, Yau AC, Norin U, Baud A, Lonnblom E, Maratou K,
            Ytterberg AJ, Ekman D, Thordardottir S, Johannesson M, Gillett A,
            Stridh P, Jagodic M, Olsson T, Fernandez-Teruel A, Zubarev RA, Mott
            R, Aitman TJ, Flint J and Holmdahl R.
  CONSRTM   EURATRANS Consortium
  TITLE     Natural polymorphisms in Tap2 influence negative selection and
            CD4ratioCD8 lineage commitment in the rat
  JOURNAL   PLoS Genet 10 (2), e1004151 (2014)
   PUBMED   24586191
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1212)
  AUTHORS   Yoon T, Macmillan H, Mortimer SE, Jiang W, Rinderknecht CH, Stern
            LJ and Mellins ED.
  TITLE     Mapping the HLA-DO/HLA-DM complex by FRET and mutagenesis
  JOURNAL   Proc Natl Acad Sci U S A 109 (28), 11276-11281 (2012)
   PUBMED   22733780
REFERENCE   3  (bases 1 to 1212)
  AUTHORS   Kim JH, Park BL, Cheong HS, Pasaje CF, Bae JS, Park JS, Uh ST, Kim
            YH, Kim MK, Choi IS, Choi BW, Park CS and Shin HD.
  TITLE     HLA-DRA polymorphisms associated with risk of nasal polyposis in
            asthmatic patients
  JOURNAL   Am J Rhinol Allergy 26 (1), 12-17 (2012)
   PUBMED   22391069
REFERENCE   4  (bases 1 to 1212)
  AUTHORS   Swaminathan S, Huentelman MJ, Corneveaux JJ, Myers AJ, Faber KM,
            Foroud T, Mayeux R, Shen L, Kim S, Turk M, Hardy J, Reiman EM and
            Saykin AJ.
  CONSRTM   Alzheimer's Disease Neuroimaging Initiative  and  NIA-LOAD/NCRAD
            Family Study Group
  TITLE     Analysis of copy number variation in Alzheimer's disease in a
            cohort of clinically characterized and neuropathologically verified
            individuals
  JOURNAL   PLoS One 7 (12), e50640 (2012)
   PUBMED   23227193
REFERENCE   5  (bases 1 to 1212)
  AUTHORS   Guo Y, Deng X, Zheng W, Xu H, Song Z, Liang H, Lei J, Jiang X, Luo
            Z and Deng H.
  TITLE     HLA rs3129882 variant in Chinese Han patients with late-onset
            sporadic Parkinson disease
  JOURNAL   Neurosci Lett 501 (3), 185-187 (2011)
   PUBMED   21791235
REFERENCE   6  (bases 1 to 1212)
  AUTHORS   Riberdy JM, Newcomb JR, Surman MJ, Barbosa JA and Cresswell P.
  TITLE     HLA-DR molecules from an antigen-processing mutant cell line are
            associated with invariant chain peptides
  JOURNAL   Nature 360 (6403), 474-477 (1992)
   PUBMED   1448172
REFERENCE   7  (bases 1 to 1212)
  AUTHORS   De Palma,J.
  TITLE     Cause & effect, or ... there are lies, damn lies, and statistics
  JOURNAL   Nephrol News Issues 6 (11), 27-57 (1992)
   PUBMED   1300424
REFERENCE   8  (bases 1 to 1212)
  AUTHORS   Holowachuk EW, Greer MK and Martin DR.
  TITLE     Elevated mRNA levels of major histocompatibility complex class II
            genes in lymphocytes of autoimmune BB rats
  JOURNAL   Diabetes 37 (12), 1637-1640 (1988)
   PUBMED   3142800
REFERENCE   9  (bases 1 to 1212)
  AUTHORS   Holowachuk EW, Greer MK and Martin DR.
  TITLE     The complete sequence of the MHC class II chain RT.1D alpha u of
            the diabetic BB rat: mRNA levels of RT1.D alpha in lymphocytes
  JOURNAL   Nucleic Acids Res 15 (24), 10551-10567 (1987)
   PUBMED   3122183
REFERENCE   10 (bases 1 to 1212)
  AUTHORS   Holowachuk,E.W.
  TITLE     Isolation and characterization of a cDNA clone for the MHC class II
            chain RT1.Du alpha of the diabetic BB rat
  JOURNAL   Immunogenetics 22 (6), 665-671 (1985)
   PUBMED   3865897
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            FM048166.1 and BC098677.1.
            
            On Sep 19, 2009 this sequence version replaced NM_001008847.1.
            
            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 :: FQ233042.1, FQ218406.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5756307, SAMEA5760383
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-34                FM048166.1         1-34
            35-1212             BC098677.1         1-1178
FEATURES             Location/Qualifiers
     source          1..1212
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="20"
                     /map="20p12"
     gene            1..1212
                     /gene="RT1-Da"
                     /gene_synonym="DA1; H2-Ea; RT1-u"
                     /note="RT1 class II, locus Da"
                     /db_xref="GeneID:294269"
                     /db_xref="RGD:1593283"
     exon            1..137
                     /gene="RT1-Da"
                     /gene_synonym="DA1; H2-Ea; RT1-u"
                     /inference="alignment:Splign:2.1.0"
     CDS             56..823
                     /gene="RT1-Da"
                     /gene_synonym="DA1; H2-Ea; RT1-u"
                     /note="MHC RT1.u-D-alpha chain; MHC class II RT1D alpha
                     chain antigen; RT1-Du alpha; MHC class II antigen RT1.D
                     alpha chain; RT1-D alpha; histocompatibility 2, class II
                     antigen E alpha"
                     /codon_start=1
                     /product="RT1 class II, locus Da precursor"
                     /protein_id="NP_001008847.1"
                     /db_xref="GeneID:294269"
                     /db_xref="RGD:1593283"
                     /translation="MATLGDLVIRFFFMAVLMSPQKSWAIREEHTIIQAEFYLSPDQN
                     GEFMFDFDGDEIFHVDIKKSETIWRLEEFAQFASFEAQGALANIAVDKANLDIMIKRS
                     NNTPDANVIPEVTVLPKSPVNLGEPNILICFIDKFSPPAVNVTWLRNGQPVTKGVSET
                     VFLPREDHLFRKFHYLTFLPSTEDYYDCEVDHWGLEEPLRKHWEFEEKTLLPETKENV
                     LCVLGLFVGLVGIVVGIVLIIKGLRKRNAVERRQGAL"
     exon            138..383
                     /gene="RT1-Da"
                     /gene_synonym="DA1; H2-Ea; RT1-u"
                     /inference="alignment:Splign:2.1.0"
     exon            384..665
                     /gene="RT1-Da"
                     /gene_synonym="DA1; H2-Ea; RT1-u"
                     /inference="alignment:Splign:2.1.0"
     exon            666..834
                     /gene="RT1-Da"
                     /gene_synonym="DA1; H2-Ea; RT1-u"
                     /inference="alignment:Splign:2.1.0"
     exon            835..1192
                     /gene="RT1-Da"
                     /gene_synonym="DA1; H2-Ea; RT1-u"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 tgattctgcc tcagtctgag atctcttctg accccaccaa acacacaaga agaaaatggc
       61 cacacttgga gacctggtga taagattttt cttcatggct gtcctcatga gcccccagaa
      121 gtcgtgggct atcagagagg agcacaccat catccaggcg gagttctatc tttcccccga
      181 ccaaaatgga gagttcatgt ttgactttga cggtgacgag attttccatg tagatattaa
      241 aaagtcagag accatctgga gacttgaaga atttgcacag tttgccagct ttgaggctca
      301 gggtgcattg gctaatatag ctgtggacaa agctaacctg gacatcatga taaagcgctc
      361 caacaacact ccagatgcca atgtgattcc agaggtgact gtactcccca aaagcccggt
      421 gaacctggga gagcccaaca tcctcatctg tttcattgac aagttctccc ctccagcggt
      481 caatgtcacc tggcttcgga acggacaacc tgtcaccaaa ggcgtgtcag agacggtgtt
      541 tctcccaagg gaggaccacc tcttccgcaa attccactat ctgaccttcc tgccctccac
      601 ggaagattac tatgactgtg aggtggatca ctggggtctg gaggagcctc tgcggaagca
      661 ctgggagttt gaagagaaaa ccctcctccc agaaactaaa gagaatgtcc tgtgtgttct
      721 cgggttgttt gtgggtctgg taggcatcgt cgtcgggatt gtgctcatca tcaagggcct
      781 tcggaaacgc aacgcagtgg aacggcgcca aggagccctg tgagatacca ggaggtgatg
      841 gcttccgtga gagctcattg aagaaatgtg ctgtgacagc atctgaggat accccttttc
      901 tcagctcttc acctcagcag agacggcatc ttctgcagtt tccaacctca agcctcgcgg
      961 cagattctct ggtctaatgt ctggctgggg ttctccgtct gcttcctgta tctatattct
     1021 attttccatc atttatagta attcctctgt ggcacatatc acagagctct tcctccgctg
     1081 cggaactttc taagaatgga ggcatcttct gttcacttac ggcttgacat ttctccaaac
     1141 tgtgttttct ttttcttttt ttcaataaat aataaacacc ttgggtcctg aaaaaaaaaa
     1201 aaaaaaaaaa aa
//
