LOCUS       NM_001001176            2602 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus TATA-box binding protein associated factor 9B (Taf9b),
            transcript variant 2, mRNA.
ACCESSION   NM_001001176
VERSION     NM_001001176.2
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 2602)
  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 2602)
  AUTHORS   He,Y., Chen,Q., Dai,J., Cui,Y., Zhang,C., Wen,X., Li,J., Xiao,Y.,
            Peng,X., Liu,M., Shen,B., Sha,J., Hu,Z., Li,J. and Shu,W.
  TITLE     Single-cell RNA-Seq reveals a highly coordinated transcriptional
            program in mouse germ cells during primordial follicle formation
  JOURNAL   Aging Cell 20 (7), e13424 (2021)
   PUBMED   34174788
REFERENCE   3  (bases 1 to 2602)
  AUTHORS   Bardot,P., Vincent,S.D., Fournier,M., Hubaud,A., Joint,M., Tora,L.
            and Pourquie,O.
  TITLE     The TAF10-containing TFIID and SAGA transcriptional complexes are
            dispensable for early somitogenesis in the mouse embryo
  JOURNAL   Development 144 (20), 3808-3818 (2017)
   PUBMED   28893950
REFERENCE   4  (bases 1 to 2602)
  AUTHORS   Herrera,F.J., Yamaguchi,T., Roelink,H. and Tjian,R.
  TITLE     Core promoter factor TAF9B regulates neuronal gene expression
  JOURNAL   Elife 3, e02559 (2014)
   PUBMED   25006164
  REMARK    GeneRIF: TAF9B also regulates neuronal gene transcription in vivo.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2602)
  AUTHORS   Koscielny,G., Yaikhom,G., Iyer,V., Meehan,T.F., Morgan,H.,
            Atienza-Herrero,J., Blake,A., Chen,C.K., Easty,R., Di Fenza,A.,
            Fiegel,T., Grifiths,M., Horne,A., Karp,N.A., Kurbatova,N.,
            Mason,J.C., Matthews,P., Oakley,D.J., Qazi,A., Regnart,J.,
            Retha,A., Santos,L.A., Sneddon,D.J., Warren,J., Westerberg,H.,
            Wilson,R.J., Melvin,D.G., Smedley,D., Brown,S.D., Flicek,P.,
            Skarnes,W.C., Mallon,A.M. and Parkinson,H.
  TITLE     The International Mouse Phenotyping Consortium Web Portal, a
            unified point of access for knockout mice and related phenotyping
            data
  JOURNAL   Nucleic Acids Res 42 (Database issue), D802-D809 (2014)
   PUBMED   24194600
REFERENCE   6  (bases 1 to 2602)
  AUTHORS   Chung,W.C., Huang,T.N. and Hsueh,Y.P.
  TITLE     Targeted deletion of CASK-interacting nucleosome assembly protein
            causes higher locomotor and exploratory activities
  JOURNAL   Neurosignals 19 (3), 128-141 (2011)
   PUBMED   21576927
  REMARK    GeneRIF: These observations suggest that although CINAP deletion in
            mice does not influence learning and memory behaviors, CINAP is
            required for restriction of locomotor and exploratory activities.
REFERENCE   7  (bases 1 to 2602)
  AUTHORS   Cox,B.J., Vollmer,M., Tamplin,O., Lu,M., Biechele,S.,
            Gertsenstein,M., van Campenhout,C., Floss,T., Kuhn,R., Wurst,W.,
            Lickert,H. and Rossant,J.
  TITLE     Phenotypic annotation of the mouse X chromosome
  JOURNAL   Genome Res 20 (8), 1154-1164 (2010)
   PUBMED   20548051
REFERENCE   8  (bases 1 to 2602)
  AUTHORS   Yokoyama,S., Ito,Y., Ueno-Kudoh,H., Shimizu,H., Uchibe,K.,
            Albini,S., Mitsuoka,K., Miyaki,S., Kiso,M., Nagai,A., Hikata,T.,
            Osada,T., Fukuda,N., Yamashita,S., Harada,D., Mezzano,V., Kasai,M.,
            Puri,P.L., Hayashizaki,Y., Okado,H., Hashimoto,M. and Asahara,H.
  TITLE     A systems approach reveals that the myogenesis genome network is
            regulated by the transcriptional repressor RP58
  JOURNAL   Dev Cell 17 (6), 836-848 (2009)
   PUBMED   20059953
REFERENCE   9  (bases 1 to 2602)
  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
            CA559941.1, BC051635.1 and BC066223.1.
            
            On Nov 21, 2009 this sequence version replaced NM_001001176.1.
            
            Transcript Variant: This variant (2) differs in the 5' UTR and
            coding sequence compared to variant 1. The resulting isoform (2) is
            shorter at the N-terminus compared to isoform 1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC066223.1, AK135097.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164138, SAMN01164142
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-202               CA559941.1         1-202
            203-2576            BC051635.1         1-2374
            2577-2602           BC066223.1         2368-2393
FEATURES             Location/Qualifiers
     source          1..2602
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="X"
                     /map="X 47.36 cM"
     gene            1..2602
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /note="TATA-box binding protein associated factor 9B"
                     /db_xref="GeneID:407786"
                     /db_xref="MGI:MGI:3039562"
     exon            1..264
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /inference="alignment:Splign:2.1.0"
     CDS             214..963
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /EC_number="2.7.4.3"
                     /note="isoform 2 is encoded by transcript variant 2;
                     TAF9-like RNA polymerase II, TATA box binding protein
                     (TBP)-associated factor; TAF9B RNA polymerase II, TATA box
                     binding protein (TBP)-associated factor; transcription
                     initiation factor TFIID subunit 9B;
                     transcription-associated factor TAFII31L"
                     /codon_start=1
                     /product="transcription initiation factor TFIID subunit 9B
                     isoform 2"
                     /protein_id="NP_001001176.2"
                     /db_xref="CCDS:CCDS30340.1"
                     /db_xref="GeneID:407786"
                     /db_xref="MGI:MGI:3039562"
                     /translation="MEPAKMAPIKNAPRDALVMAQILKDMGITEYEPRVINQMLEFAF
                     RYVTTILDDAKIYSSHAKKPTVDADDVRLAIQCRADQSFTSPPPRDFLLDIARQKNQT
                     PLPLIKPYAGPRLPPDRYCLTAPNYRLKSLVKKGPNQGRLVPRLSAVSSRPTTPPVAP
                     PQAVSGPNKAATPVSVTSQRFAVQIPPSQSTPAKPAPAATAVQNVLINPSMIGPKNIL
                     ITTSMVSSQNTATDSNPLKRKHDDDDDNDTM"
     exon            265..346
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /inference="alignment:Splign:2.1.0"
     exon            347..483
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /inference="alignment:Splign:2.1.0"
     exon            484..618
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /inference="alignment:Splign:2.1.0"
     exon            619..688
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /inference="alignment:Splign:2.1.0"
     exon            689..799
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /inference="alignment:Splign:2.1.0"
     exon            800..2583
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /inference="alignment:Splign:2.1.0"
     regulatory      966..971
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /note="hexamer: AATAAA"
     polyA_site      991
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /note="major polyA site"
     regulatory      2558..2563
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /note="hexamer: AATAAA"
     polyA_site      2576
                     /gene="Taf9b"
                     /gene_synonym="Taf9l"
                     /note="major polyA site"
ORIGIN      
        1 cgctagggcg acttcctccg cacctctcca cctccgaacc tgcatgggcc ccgggtagcc
       61 aagtccacac aggtgggggc tggcggctgg gaagcagccc cggccgggga gctgcgtgct
      121 aggaccgcct tccatccccc acaggggtgg agccagaccg aggtggaaac cgcctgcagc
      181 tctatctccg aggttgagga gccgcaagag aaaatggagc cggccaagat ggcgcctatc
      241 aagaacgctc cgagagatgc cttggtgatg gcacagatcc tgaaggatat gggaatcaca
      301 gagtatgagc caagggttat aaatcaaatg ttggaatttg ctttccgata tgtgactaca
      361 attctggacg atgcaaagat ttattcgagt catgctaaga aacccactgt tgatgccgat
      421 gacgtgagac tggccatcca gtgtcgggct gaccagtcct ttacctctcc tcccccaaga
      481 gattttttac tagatattgc aaggcagaag aatcaaaccc ctttgccgct gattaagcca
      541 tatgcaggac ccagactgcc acctgataga tactgcttaa cagctccaaa ctataggctg
      601 aagtccttag ttaaaaaggg acctaaccaa ggaagactag tgcctagatt aagtgcggtc
      661 agtagtagac caactactcc tcctgtagca cccccacaag cagtatctgg cccaaataag
      721 gctgcaactc cggtgtcagt gacaagccaa agatttgctg tgcagattcc accttctcag
      781 tccacacctg ccaagccagc tcctgcagca actgcagtcc aaaatgttct gattaatcct
      841 tcaatgattg ggcccaaaaa tattctcatt accaccagca tggtttcctc acagaacaca
      901 gccaccgact caaacccact gaagaggaag catgatgacg acgatgacaa tgacaccatg
      961 taaggaataa agtctgttct gcatacatta acatttttgt gtgtttgggc ccatatggcg
     1021 gactcaatag cctaagtctt cataagtttt atcttagaaa cgtagtagta atatttttca
     1081 cattagttac atctggaagg ttttgttaca gtacaagtac ttgcttctag acagcttcat
     1141 taatgttgag tctcaccatg gcaactctgt ttttagaagc agttttccga tatgtgtcac
     1201 tagcagcagc gcttggactt cagctcctgg tctcatttac atttaacagg actttctttt
     1261 gatagtgaac tattcacatt gtcacttttt gaccaaatct ctcaatttag gaaccaaatc
     1321 tctcaattta ggaaactttt ttttttttga agagtggatt tagaagtgtg ctaaatccat
     1381 tttgaatgta tttgggtttt ggtcttttct gatttcctat ctagatctcg tttgttttct
     1441 gttcccacct ctcatcgcct taagtcattt gccattgcac ttaaatgtaa tagactgtga
     1501 ctggaatgtg taatatgccc tagatgcctg gcactctgca gttcctgtga accggagtgt
     1561 ctgcttttgc tcttcttcac tcctaacaga gcattcgggt ctcagcactt gcctttcatg
     1621 cctgctaagc acttctcatt gataggcact tttgcatcaa ttgcattcac aatctttcat
     1681 gtttaaaatt taaaatataa cttaaaacct gccttggaaa gtaatttaca ctggactcag
     1741 acaaaaccac taaagaactt tgttgttttt cttaaccacc tgcatatata tatgctttgg
     1801 tcactacggc ttgaaccagt ccgttggttt cattcagacc acctttctag cttgctgctg
     1861 agggtgtcac acataagatg ggatcaagcc tgaaggaaga ttctgattct ctttccctat
     1921 caggccaaca gggaaaagtc acctgactcc atttaggtac cccaaaattt cccaaccatg
     1981 tttctataca ccttcttcta ctctgttaat acatacgtac aagactcact gggaacaaca
     2041 gcaaagcttt tttccaagta taaaaagaac tgatttgatt tggtttaagt tccacatagc
     2101 caacattgga aaaactttct gaaaccttca tgccacttaa aatttatagc catggatcat
     2161 caaaacttac taagtatcag catagggtgg tgtttgacac atgaaataga tcagtaacaa
     2221 gacagagata tttcatgcca gttttaattg tctaggacgg ttagtgaaag ctgatctgat
     2281 caataccata agagaaatgt gcagtataca acacagatgt caggactaga atgttctcag
     2341 ggaggcagaa tacaagaaag cctaggttct ggtattagtt tcatttacca acaatgtgac
     2401 cttactttac ctcggagcct tgttctcact agtaataggg aaataacatc taccctgcct
     2461 acctcacagg gatgttgtga gggtttagct ggtgtgtgtg aaagttccaa gattgtaaaa
     2521 gctatataat tattaatata tttgtttcaa cattgttaat aaaaatttaa ctttaatcat
     2581 taaaaaaaaa aaaaaaaaaa aa
//
