LOCUS       NM_001008846            1404 bp    mRNA    linear   ROD 30-MAR-2024
DEFINITION  Rattus norvegicus RT1 class II, locus DOb (RT1-DOb), transcript
            variant 1, mRNA.
ACCESSION   NM_001008846 XM_345085
VERSION     NM_001008846.2
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 1404)
  AUTHORS   Tuncel,J., Haag,S., Yau,A.C., Norin,U., Baud,A., Lonnblom,E.,
            Maratou,K., Ytterberg,A.J., Ekman,D., Thordardottir,S.,
            Johannesson,M., Gillett,A., Stridh,P., Jagodic,M., Olsson,T.,
            Fernandez-Teruel,A., Zubarev,R.A., Mott,R., Aitman,T.J., 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 1404)
  AUTHORS   Yoon,T., Macmillan,H., Mortimer,S.E., Jiang,W., Rinderknecht,C.H.,
            Stern,L.J. and Mellins,E.D.
  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 1404)
  AUTHORS   Gunther,E. and Walter,L.
  TITLE     The major histocompatibility complex of the rat (Rattus norvegicus)
  JOURNAL   Immunogenetics 53 (7), 520-542 (2001)
   PUBMED   11685465
  REMARK    Review article
REFERENCE   4  (bases 1 to 1404)
  AUTHORS   Koda,T., Kishi,M., Kakinuma,M. and Tank,W.R.
  TITLE     Genomic organization and cDNA sequence of the rat RT1-DOb gene
  JOURNAL   Immunogenetics 48 (1), 67-72 (1998)
   PUBMED   9601947
REFERENCE   5  (bases 1 to 1404)
  AUTHORS   Liljedahl,M., Winqvist,O., Surh,C.D., Wong,P., Ngo,K., Teyton,L.,
            Peterson,P.A., Brunmark,A., Rudensky,A.Y., Fung-Leung,W.P. and
            Karlsson,L.
  TITLE     Altered antigen presentation in mice lacking H2-O
  JOURNAL   Immunity 8 (2), 233-243 (1998)
   PUBMED   9492004
REFERENCE   6  (bases 1 to 1404)
  AUTHORS   Liljedahl,M., Kuwana,T., Fung-Leung,W.P., Jackson,M.R.,
            Peterson,P.A. and Karlsson,L.
  TITLE     HLA-DO is a lysosomal resident which requires association with
            HLA-DM for efficient intracellular transport
  JOURNAL   EMBO J 15 (18), 4817-4824 (1996)
   PUBMED   8890155
REFERENCE   7  (bases 1 to 1404)
  AUTHORS   Scholler,J. and Lernmark,A.
  TITLE     Isolation of a rat immune response gene identical to an alleged
            mouse a class II beta-chain pseudogene
  JOURNAL   Immunogenetics 22 (6), 601-608 (1985)
   PUBMED   3865893
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000020.1.
            
            On Sep 23, 2022 this sequence version replaced NM_001008846.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26643292.63162.1, KC222915.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN16676811 [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
            1-155               JAXUCZ010000020.1  4627369-4627523     c
            156-425             JAXUCZ010000020.1  4625256-4625525     c
            426-707             JAXUCZ010000020.1  4623340-4623621     c
            708-818             JAXUCZ010000020.1  4622302-4622412     c
            819-847             JAXUCZ010000020.1  4622059-4622087     c
            848-1404            JAXUCZ010000020.1  4621336-4621892     c
FEATURES             Location/Qualifiers
     source          1..1404
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="20"
                     /map="20p12"
     gene            1..1404
                     /gene="RT1-DOb"
                     /gene_synonym="DOb; H2-Ob; RT1-Bb2"
                     /note="RT1 class II, locus DOb"
                     /db_xref="GeneID:365542"
                     /db_xref="RGD:1595814"
     exon            1..155
                     /gene="RT1-DOb"
                     /gene_synonym="DOb; H2-Ob; RT1-Bb2"
                     /inference="alignment:Splign:2.1.0"
     CDS             65..883
                     /gene="RT1-DOb"
                     /gene_synonym="DOb; H2-Ob; RT1-Bb2"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; histocompatibility 2, O region beta locus; RT1
                     class II, DO beta"
                     /codon_start=1
                     /product="RT1 class II, DO beta isoform 1 precursor"
                     /protein_id="NP_001008846.1"
                     /db_xref="GeneID:365542"
                     /db_xref="RGD:1595814"
                     /translation="MGAGRAPWVVALLVNLMRPDSFMVEGRDSPEDFVIQAKAECYFT
                     NGTEKVRFLVRFIFNLEEYLHFDSDLGFFVALTELGEVDADQWNKRLDLLETSRAAVN
                     MVCRQEYKLGAPFTVERNVPPEVTVYPERTPLLQQHNLLLCSVTDFYPGDISVRWFRN
                     GQEERSGVMSTGLVRNGDWTFQTTVMLEMIPELGDVYSCLVEHPGLLRPVSVAWVAQS
                     EYSWEKILSGAAAFLLGLTVFLVGAVIHLKAQKASVETQPGNEASRALLPPHPY"
     exon            156..425
                     /gene="RT1-DOb"
                     /gene_synonym="DOb; H2-Ob; RT1-Bb2"
                     /inference="alignment:Splign:2.1.0"
     exon            426..707
                     /gene="RT1-DOb"
                     /gene_synonym="DOb; H2-Ob; RT1-Bb2"
                     /inference="alignment:Splign:2.1.0"
     exon            708..818
                     /gene="RT1-DOb"
                     /gene_synonym="DOb; H2-Ob; RT1-Bb2"
                     /inference="alignment:Splign:2.1.0"
     exon            819..847
                     /gene="RT1-DOb"
                     /gene_synonym="DOb; H2-Ob; RT1-Bb2"
                     /inference="alignment:Splign:2.1.0"
     exon            848..1404
                     /gene="RT1-DOb"
                     /gene_synonym="DOb; H2-Ob; RT1-Bb2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gtggaagaca gctccattct aaagaggtgt atcagtctct tattgtccct tggtcccctc
       61 cagaatgggt gctgggaggg ccccctgggt ggtggctctg ctagtgaacc tcatgaggcc
      121 agattccttc atggttgaag gcagagactc cccagaggat tttgtgattc aggcgaaggc
      181 agagtgttac ttcaccaacg gtacagaaaa ggtccgcttc ctggtcaggt tcatcttcaa
      241 cctggaggag tacttacatt tcgacagtga cctggggttt ttcgtggcac tgacggagct
      301 gggggaggtg gacgctgatc agtggaacaa acgcctggat ctcctggaaa caagtagagc
      361 tgctgtgaac atggtctgca ggcaagagta caagctgggg gcccccttca ccgtggagag
      421 aaatgtgcct ccggaggtga cggtgtaccc agagaggacc ccattgctgc agcagcacaa
      481 cctgttgctc tgctctgtga cagacttcta ccctggggac ataagtgtca ggtggttccg
      541 gaatgggcag gaggagaggt ccggggtcat gtccactggc cttgttagga atggagactg
      601 gaccttccag acgacggtaa tgctggaaat gatcccagag cttggagacg tctacagttg
      661 ccttgtggag caccccggcc tcctgagacc tgtttctgtg gcatgggtgg ctcagtctga
      721 atattcctgg gaaaagatac tgagtggagc tgcagcattc ctgcttgggc tgactgtctt
      781 tctggtggga gctgtcatcc acctcaaggc tcagaaagcg tccgtggaga ctcagcctgg
      841 caatgaggct tcaagggcgc ttctcccacc tcacccctac taagatccta atggaagctt
      901 ctcccccaga gcctgaagaa gtgtgaaaag gctggggacc cgggttgggt aaagaatgct
      961 ggccgaaggg tctgtgagat gtggtcatgg atcttcccct tctgctctgc acctcagtac
     1021 cccctcattt tcaggatgtg gtccagaaac ttccttagga cctaacccgt tccagatcta
     1081 agttgctttg gtctctgtgg ctcaacccta accctgtgac tgggataccc ccggcctctc
     1141 tgtctcccaa ccccagcttc tagtcttcca tacagttgcc ttaaaatcct cgtcagaaag
     1201 taaaacagtc acaggtaacc acagtgaatg tataattcaa tgacttattc aaggcaaaac
     1261 ccatgtaatc acctgctcag gttaaaaaaa aaaatcaggg cagaaggaac acccattcag
     1321 agcctgcccc acatgtggcc catacatata cagccaccca attagacaag atggatgaag
     1381 caaagaagtg caggctgaca ggag
//
