LOCUS       NM_027261               1381 bp    mRNA    linear   ROD 07-OCT-2024
DEFINITION  Mus musculus TATA-box binding protein associated factor, RNA
            polymerase I, D (Taf1d), transcript variant 3, mRNA.
ACCESSION   NM_027261
VERSION     NM_027261.3
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 1381)
  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 1381)
  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 1381)
  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 1381)
  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 1381)
  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, AK012662.1 and CB523122.1.
            
            On Sep 3, 2009 this sequence version replaced NM_027261.2.
            
            Transcript Variant: This variant (3) contains a different segment
            in the 3' coding region, compared to variant 2. The resulting
            protein (isoform 3) has a shorter and distinct C-terminus when it
            is compared to isoform 2.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK012662.1, BY715713.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849375, SAMN00849380
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-49                BU850945.1         5-53
            50-1052             AK012662.1         2-1004
            1053-1381           CB523122.1         133-461
FEATURES             Location/Qualifiers
     source          1..1381
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="9"
                     /map="9 4.78 cM"
     gene            1..1381
                     /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"
     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"
     CDS             97..969
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="isoform 3 is encoded by transcript variant 3; TATA
                     box-binding protein-associated factor RNA polymerase I
                     subunit D; TBP-associated factor 1D; TATA box binding
                     protein (Tbp)-associated factor, RNA polymerase I, D; TATA
                     box-binding protein-associated factor 1D; transcription
                     initiation factor SL1/TIF-IB subunit D; Josephin domain
                     containing 3"
                     /codon_start=1
                     /product="TATA box-binding protein-associated factor RNA
                     polymerase I subunit D isoform 3"
                     /protein_id="NP_081537.1"
                     /db_xref="CCDS:CCDS52726.1"
                     /db_xref="GeneID:75316"
                     /db_xref="MGI:MGI:1922566"
                     /translation="

MAQSEVNSVCVASDRAGDTGDQSDDSSDGSLFKTQCAPSPIQKQRHPTVKRVTLPASVETDSSSDSSIEPRPLTLKAIFERFKKKKRKKRKKRKYEPKLRPRGRPRGKPSGTRITRRSQIDAKQIKDKGAVFPFLESESGRKPLPWKKILTYEQAVARGFFHHIEKLKYEHHLKECLKQMHAGEDLEKEDLDSRRHKYMDDDGSLSPIEEPLTEDEATNPQAECDIKLVEDSCFIISSEFSRKRNLEQEKIKKESTFSKKAKDATHREKGHRRTLKGNEHVTIEEGKEHR"

     misc_feature    97..306
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9D4V4.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    163..165
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="Phosphoserine.
                     /evidence=ECO:0000250|UniProtKB:Q9H5J8; propagated from
                     UniProtKB/Swiss-Prot (Q9D4V4.2); phosphorylation site"
     misc_feature    187..825
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="TATA box-binding protein-associated factor 1D;
                     Region: TAF1D; pfam15333"
                     /db_xref="CDD:464653"
     misc_feature    340..444
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9D4V4.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    505..507
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="Phosphoserine.
                     /evidence=ECO:0000250|UniProtKB:Q9H5J8; propagated from
                     UniProtKB/Swiss-Prot (Q9D4V4.2); phosphorylation site"
     misc_feature    688..753
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9D4V4.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    790..792
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="Phosphoserine.
                     /evidence=ECO:0000250|UniProtKB:Q9H5J8; propagated from
                     UniProtKB/Swiss-Prot (Q9D4V4.2); phosphorylation site"
     misc_feature    865..924
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9D4V4.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     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..1362
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1341..1346
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="hexamer: AATAAA"
     polyA_site      1362
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="major polyA site"
ORIGIN      

gcgagatttcgtccttgtcctagtccggctgctgggcgccgggagcgctcttttcgacgcggcggaagagaaaattgggaaaggccgcgaaaagtgatggctcaatcagaagtgaattctgtctgtgtggcatcggatagagctggagatactggagaccaaagtgatgactcctctgatggcagcttatttaaaactcagtgtgctccttcacctatacaaaagcaaagacaccctactgtgaaacgtgttactttacctgcaagtgttgaaacagattcatcaagtgactcttctatagaaccaaggcctctgactttaaaggctatttttgaaagatttaaaaaaaagaaacggaaaaagaggaaaaagagaaaatatgagccaaaattaagaccaagaggaagaccaagaggaaaaccatcgggaacgaggatcactagaaggtcgcaaatagatgcaaaacaaattaaagacaaaggagctgtgtttccattcttagaatctgagagtggaagaaaacctttaccttggaagaaaattttaacatatgagcaagctgttgcaagaggattttttcaccacattgaaaaactcaagtatgaacaccaccttaaggaatgcttgaagcaaatgcatgctggggaagatttagaaaaggaagaccttgacagtcggaggcacaaatacatggatgatgatggttcactttctcctattgaagagccattaactgaagatgaagcaacaaatcctcaggctgaatgtgatatcaagttggttgaagacagttgcttcataataagttcagaattctcaaggaagagaaacttggaacaagagaagattaagaaagaatctacattttctaaaaaagccaaagatgccacacacagagagaaagggcacagaagaaccttgaaaggaaatgaacatgtgactattgaagaaggtaaagaacatagataacagtgtatgccaagtagatcaagaactaatctggggaagaagataaacttgctggtggaacgctaataaatacttagtaaagcttttttcgttgcttgatttcagagtaagaaatactataaggattattttactactatagtaaacatgattgtgattctggaaggaaaatgctaacaatcctatacatgtctagattcaagaccccagcctcgcccttttgctcatctgcagagcaaggtcatgaagaaaggagagttagagtatctggaggttcaccacctctgtggtctgtcgcagccactatgactatgaggaggaagagatgatttgaaaattggattaaactcctggactcttatactagaaaaaataaactaatgataaaacccaaaaaaaaaaaaaaaaaaaa

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