LOCUS       NM_029248               1148 bp    mRNA    linear   ROD 19-DEC-2023
DEFINITION  Mus musculus TATA-box binding protein associated factor, RNA
            polymerase I, D (Taf1d), transcript variant 2, mRNA.
ACCESSION   NM_029248
VERSION     NM_029248.2
KEYWORDS    RefSeq; RefSeq Select.
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 1148)
  AUTHORS   Tscherner AK, McClatchie T, Macaulay AD and Baltz JM.
  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   2  (bases 1 to 1148)
  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   3  (bases 1 to 1148)
  AUTHORS   Murano K, Okuwaki M, Momose F, Kumakura M, Ueshima S, Newbold RF
            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   4  (bases 1 to 1148)
  AUTHORS   Stryke D, Kawamoto M, Huang CC, Johns SJ, King LA, Harper CA, Meng
            EC, Lee RE, Yee A, L'Italien L, Chuang PT, Young SG, Skarnes WC,
            Babbitt PC and Ferrin TE.
  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, AK016109.1, BC117070.1 and AU044383.1.
            
            On Sep 3, 2009 this sequence version replaced NM_029248.1.
            
            Transcript Variant: This variant (2) encodes the longer protein
            (isoform 2).
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK016109.1, SRR7345562.2422681.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849383, SAMN00849384
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-46                BU850945.1         5-50
            47-921              AK016109.1         1-875
            922-1093            BC117070.1         854-1025
            1094-1148           AU044383.1         1-55                c
FEATURES             Location/Qualifiers
     source          1..1148
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="9"
                     /map="9 4.78 cM"
     gene            1..1148
                     /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..1065
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /note="isoform 2 is encoded by transcript variant 2; 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 2"
                     /protein_id="NP_083524.2"
                     /db_xref="CCDS:CCDS22836.1"
                     /db_xref="GeneID:75316"
                     /db_xref="MGI:MGI:1922566"
                     /translation="

MAQSEVNSVCVASDRAGDTGDQSDDSSDGSLFKTQCAPSPIQKQRHPTVKRVTLPASVETDSSSDSSIEPRPLTLKAIFERFKKKKRKKRKKRKYEPKLRPRGRPRGKPSGTRITRRSQIDAKQIKDKGAVFPFLESESGRKPLPWKKILTYEQAVARGFFHHIEKLKYEHHLKECLKQMHAGEDLEKEDLDSRRHKYMDDDGSLSPIEEPLTEDEATNPQAECDIKLVEDSCFIISSEFSRKRNLEQEKIKKESTFSKKAKDATHREKGHRRTLKGNEHVTIEEDSRPQPRPFAHLQSKVMKKGELEYLEVHHLCGLSQPL"

     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:434642"
     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..952
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
     exon            953..1148
                     /gene="Taf1d"
                     /gene_synonym="2810003M17Rik; 4930553M18Rik;
                     5930426I11Rik; Josd3; TAF(I)41; TAFI41"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcgagatttcgtccttgtcctagtccggctgctgggcgccgggagcgctcttttcgacgcggcggaagagaaaattgggaaaggccgcgaaaagtgatggctcaatcagaagtgaattctgtctgtgtggcatcggatagagctggagatactggagaccaaagtgatgactcctctgatggcagcttatttaaaactcagtgtgctccttcacctatacaaaagcaaagacaccctactgtgaaacgtgttactttacctgcaagtgttgaaacagattcatcaagtgactcttctatagaaccaaggcctctgactttaaaggctatttttgaaagatttaaaaaaaagaaacggaaaaagaggaaaaagagaaaatatgagccaaaattaagaccaagaggaagaccaagaggaaaaccatcgggaacgaggatcactagaaggtcgcaaatagatgcaaaacaaattaaagacaaaggagctgtgtttccattcttagaatctgagagtggaagaaaacctttaccttggaagaaaattttaacatatgagcaagctgttgcaagaggattttttcaccacattgaaaaactcaagtatgaacaccaccttaaggaatgcttgaagcaaatgcatgctggggaagatttagaaaaggaagaccttgacagtcggaggcacaaatacatggatgatgatggttcactttctcctattgaagagccattaactgaagatgaagcaacaaatcctcaggctgaatgtgatatcaagttggttgaagacagttgcttcataataagttcagaattctcaaggaagagaaacttggaacaagagaagattaagaaagaatctacattttctaaaaaagccaaagatgccacacacagagagaaagggcacagaagaaccttgaaaggaaatgaacatgtgactattgaagaagattcaagaccccagcctcgcccttttgctcatctgcagagcaaggtcatgaagaaaggagagttagagtatctggaggttcaccacctctgtggtctgtcgcagccactatgactatgaggaggaagagatgatttgaaaattggattaaactcctggactcttatactagaaaaaataaactaatgataaaaccc

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