LOCUS       NR_028401               1289 bp    RNA     linear   ROD 30-APR-2024
DEFINITION  Mus musculus TATA-box binding protein associated factor, RNA
            polymerase I, D (Taf1d), transcript variant 1, non-coding RNA.
ACCESSION   NR_028401
VERSION     NR_028401.1
KEYWORDS    RefSeq.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 1289)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 1289)
  AUTHORS   Tscherner,A.K., McClatchie,T., Macaulay,A.D. and Baltz,J.M.
  TITLE     Relationship of quantitative reverse transcription polymerase chain
            reaction (RT-PCR) to RNA Sequencing (RNAseq) transcriptome
            identifies mouse preimplantation embryo reference genesdagger
  JOURNAL   Biol Reprod 109 (5), 601-617 (2023)
   PUBMED   37669129
REFERENCE   3  (bases 1 to 1289)
  AUTHORS   Percharde,M., Wong,P. and Ramalho-Santos,M.
  TITLE     Global Hypertranscription in the Mouse Embryonic Germline
  JOURNAL   Cell Rep 19 (10), 1987-1996 (2017)
   PUBMED   28591571
REFERENCE   4  (bases 1 to 1289)
  AUTHORS   Murano,K., Okuwaki,M., Momose,F., Kumakura,M., Ueshima,S.,
            Newbold,R.F. and Nagata,K.
  TITLE     Reconstitution of human rRNA gene transcription in mouse cells by a
            complete SL1 complex
  JOURNAL   J Cell Sci 127 (Pt 15), 3309-3319 (2014)
   PUBMED   24928901
REFERENCE   5  (bases 1 to 1289)
  AUTHORS   Stryke,D., Kawamoto,M., Huang,C.C., Johns,S.J., King,L.A.,
            Harper,C.A., Meng,E.C., Lee,R.E., Yee,A., L'Italien,L.,
            Chuang,P.T., Young,S.G., Skarnes,W.C., Babbitt,P.C. and Ferrin,T.E.
  TITLE     BayGenomics: a resource of insertional mutations in mouse embryonic
            stem cells
  JOURNAL   Nucleic Acids Res 31 (1), 278-281 (2003)
   PUBMED   12520002
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BU850945.1, AK050165.1 and AK014920.1.
            
            Transcript Variant: This variant (1) lacks an alternate internal
            exon and contains additional 3' exons, compared to variant 2. This
            variant is represented as non-coding because the use of the 5'-most
            expected translational start codon, as used in variant 2, renders
            the transcript a candidate for nonsense-mediated mRNA decay (NMD).
            
            ##Evidence-Data-START##
            RNAseq introns :: single sample supports all introns SAMN00849380,
                              SAMN00849381 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-46                BU850945.1         5-50
            47-1262             AK050165.1         3-1218
            1263-1289           AK014920.1         1215-1241
FEATURES             Location/Qualifiers
     source          1..1289
                     /organism="Mus musculus"
                     /mol_type="transcribed RNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="9"
                     /map="9 4.78 cM"
     gene            1..1289
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="TATA-box binding protein associated factor, RNA
                     polymerase I, D"
                     /db_xref="GeneID:75316"
                     /db_xref="MGI:MGI:1922566"
     misc_RNA        1..1289
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /product="TATA-box binding protein associated factor, RNA
                     polymerase I, D, transcript variant 1"
                     /db_xref="GeneID:75316"
                     /db_xref="MGI:MGI:1922566"
     exon            1..70
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            71..164
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    97..963
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="COORDINATES:
                     alignment:Blast2seq::RefSeq|NM_027261.3"
                     /note="primary ORF has stop codon >50 nucleotides from the
                     terminal splice site; nonsense-mediated decay (NMD)
                     candidate"
     exon            165..555
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            556..731
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            732..783
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            784..952
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            953..1015
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            1016..1058
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            1059..1092
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            1093..1122
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            1123..1180
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            1181..1289
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcgagatttcgtccttgtcctagtccggctgctgggcgccgggagcgctcttttcgacgcggcggaagagaaaattgggaaaggccgcgaaaagtgatggctcaatcagaagtgaattctgtctgtgtggcatcggatagagctggagatactggagaccaaagtgatgactcctctgatggcagcttatttaaaactcagtgtgctccttcacctatacaaaagcaaagacaccctactgtgaaacgtgttactttacctgcaagtgttgaaacagattcatcaagtgactcttctatagaaccaaggcctctgactttaaaggctatttttgaaagatttaaaaaaaagaaacggaaaaagaggaaaaagagaaaatatgagccaaaattaagaccaagaggaagaccaagaggaaaaccatcgggaacgaggatcactagaaggtcgcaaatagatgcaaaacaaattaaagacaaaggagctgtgtttccattcttagaatctgagagtggaagaaaacctttaccttggaagaaaattttaacatatgagcaagctgttgcaagaggattttttcaccacattgaaaaactcaagtatgaacaccaccttaaggaatgcttgaagcaaatgcatgctggggaagatttagaaaaggaagaccttgacagtcggaggcacaaatacatggatgatgatggttcactttctcctattgaagagccattaactgaagatgaagcaacaaatcctcaggctgaatgtgatatcaagttggttgaagacagttgcttcataataagttcagaattctcaaggaagagaaacttggaacaagagaagattaagaaagaatctacattttctaaaaaagccaaagatgccacacacagagagaaagggcacagaagaaccttgaaaggaaatgaacatgtgactattgaagaaggcttgtcttgattatgaagtcagaattggaagatacccatgaatggatgtttgtttcagtgttgcactggcacttccttcataaagattagagttgtgagtgtgaggaatggatatgagaagaccctaaagagatgtttgggtgacacgagtgaaccctaccctaaaatggtttaaagataacatgaagggtccttaaaataaattgaagaaatcctcaaatcttctggtgacctggatggacagcaaaggaatcaaatccctcaaataatttatttgacttaaattaaaaataaataaatatatacagtaaaaagaaccttttatagtttgtatgt

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