LOCUS       NM_001127690            4736 bp    mRNA    linear   ROD 31-MAR-2024
DEFINITION  Rattus norvegicus upstream binding transcription factor (Ubtf),
            transcript variant 2, mRNA.
ACCESSION   NM_001127690
VERSION     NM_001127690.2
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 4736)
  AUTHORS   Edvardson,S., Nicolae,C.M., Agrawal,P.B., Mignot,C., Payne,K.,
            Prasad,A.N., Prasad,C., Sadler,L., Nava,C., Mullen,T.E.,
            Begtrup,A., Baskin,B., Powis,Z., Shaag,A., Keren,B., Moldovan,G.L.
            and Elpeleg,O.
  TITLE     Heterozygous De Novo UBTF Gain-of-Function Variant Is Associated
            with Neurodegeneration in Childhood
  JOURNAL   Am J Hum Genet 101 (2), 267-273 (2017)
   PUBMED   28777933
REFERENCE   2  (bases 1 to 4736)
  AUTHORS   Sun,X., Chen,H., Deng,Z., Hu,B., Luo,H., Zeng,X., Han,L., Cai,G.
            and Ma,L.
  TITLE     The Warsaw breakage syndrome-related protein DDX11 is required for
            ribosomal RNA synthesis and embryonic development
  JOURNAL   Hum Mol Genet 24 (17), 4901-4915 (2015)
   PUBMED   26089203
REFERENCE   3  (bases 1 to 4736)
  AUTHORS   Nonnekens,J., Perez-Fernandez,J., Theil,A.F., Gadal,O., Bonnart,C.
            and Giglia-Mari,G.
  TITLE     Mutations in TFIIH causing trichothiodystrophy are responsible for
            defects in ribosomal RNA production and processing
  JOURNAL   Hum Mol Genet 22 (14), 2881-2893 (2013)
   PUBMED   23562818
REFERENCE   4  (bases 1 to 4736)
  AUTHORS   Knutson,B.A. and Hahn,S.
  TITLE     TFIIB-related factors in RNA polymerase I transcription
  JOURNAL   Biochim Biophys Acta 1829 (3-4), 265-273 (2013)
   PUBMED   22960599
  REMARK    Review article
REFERENCE   5  (bases 1 to 4736)
  AUTHORS   Brehm,M.A., Wundenberg,T., Williams,J., Mayr,G.W. and Shears,S.B.
  TITLE     A non-catalytic role for inositol 1,3,4,5,6-pentakisphosphate
            2-kinase in the synthesis of ribosomal RNA
  JOURNAL   J Cell Sci 126 (Pt 2), 437-444 (2013)
   PUBMED   23203802
REFERENCE   6  (bases 1 to 4736)
  AUTHORS   Lin,C.Y., Tuan,J., Scalia,P., Bui,T. and Comai,L.
  TITLE     The cell cycle regulatory factor TAF1 stimulates ribosomal DNA
            transcription by binding to the activator UBF
  JOURNAL   Curr Biol 12 (24), 2142-2146 (2002)
   PUBMED   12498690
REFERENCE   7  (bases 1 to 4736)
  AUTHORS   Sutherland,H.G., Mumford,G.K., Newton,K., Ford,L.V., Farrall,R.,
            Dellaire,G., Caceres,J.F. and Bickmore,W.A.
  TITLE     Large-scale identification of mammalian proteins localized to
            nuclear sub-compartments
  JOURNAL   Hum Mol Genet 10 (18), 1995-2011 (2001)
   PUBMED   11555636
REFERENCE   8  (bases 1 to 4736)
  AUTHORS   Pelletier,G., Stefanovsky,V.Y., Faubladier,M.,
            Hirschler-Laszkiewicz,I., Savard,J., Rothblum,L.I., Cote,J. and
            Moss,T.
  TITLE     Competitive recruitment of CBP and Rb-HDAC regulates UBF
            acetylation and ribosomal transcription
  JOURNAL   Mol Cell 6 (5), 1059-1066 (2000)
   PUBMED   11106745
  REMARK    GeneRIF: competitive recruitment of CBP and Rb-HDAC regulates UBF
            acetylation and ribosomal transcription
REFERENCE   9  (bases 1 to 4736)
  AUTHORS   Ridsdale,R.A., Semotok,J.L., Larson,D.E., Rothblum,L.I. and
            Harauz,G.
  TITLE     Topology of recombinant rat upstream binding factor
  JOURNAL   Biochem Cell Biol 76 (4), 649-655 (1998)
   PUBMED   10099786
REFERENCE   10 (bases 1 to 4736)
  AUTHORS   O'Mahony,D.J. and Rothblum,L.I.
  TITLE     Identification of two forms of the RNA polymerase I transcription
            factor UBF
  JOURNAL   Proc Natl Acad Sci U S A 88 (8), 3180-3184 (1991)
   PUBMED   2014238
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000010.1.
            
            On Apr 15, 2014 this sequence version replaced NM_001127690.1.
            
            Transcript Variant: This variant (2) includes an alternate exon in
            the coding region compared to variant 1. The resulting protein
            (isoform 2) is longer but has the same N- and C-termini compared to
            isoform 1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26643287.25773.1,
                                           SRR26643429.39244.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760386,
                                           SAMEA5760393 [ECO:0006172]
            ##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
            1-143               JAXUCZ010000010.1  87772946-87773088   c
            144-268             JAXUCZ010000010.1  87770472-87770596   c
            269-444             JAXUCZ010000010.1  87768972-87769147   c
            445-528             JAXUCZ010000010.1  87768371-87768454   c
            529-684             JAXUCZ010000010.1  87768121-87768276   c
            685-749             JAXUCZ010000010.1  87765900-87765964   c
            750-870             JAXUCZ010000010.1  87765521-87765641   c
            871-981             JAXUCZ010000010.1  87765068-87765178   c
            982-1115            JAXUCZ010000010.1  87764586-87764719   c
            1116-1257           JAXUCZ010000010.1  87764320-87764461   c
            1258-1299           JAXUCZ010000010.1  87763987-87764028   c
            1300-1413           JAXUCZ010000010.1  87763782-87763895   c
            1414-1569           JAXUCZ010000010.1  87763526-87763681   c
            1570-1725           JAXUCZ010000010.1  87763020-87763175   c
            1726-1836           JAXUCZ010000010.1  87762823-87762933   c
            1837-1925           JAXUCZ010000010.1  87762365-87762453   c
            1926-2115           JAXUCZ010000010.1  87762084-87762273   c
            2116-2163           JAXUCZ010000010.1  87761194-87761241   c
            2164-2235           JAXUCZ010000010.1  87761031-87761102   c
            2236-2379           JAXUCZ010000010.1  87760797-87760940   c
            2380-4736           JAXUCZ010000010.1  87758346-87760702   c
FEATURES             Location/Qualifiers
     source          1..4736
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="10"
                     /map="10q32.1"
     gene            1..4736
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /note="upstream binding transcription factor"
                     /db_xref="GeneID:25574"
                     /db_xref="RGD:3927"
     exon            1..143
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            144..268
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     CDS             211..2505
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /note="isoform 2 is encoded by transcript variant 2;
                     nucleolar transcription factor 1; UBF-1; upstream-binding
                     factor 1; transcription factor UBF; upstream binding
                     transcription factor, RNA polymerase I"
                     /codon_start=1
                     /product="nucleolar transcription factor 1 isoform 2"
                     /protein_id="NP_001121162.1"
                     /db_xref="GeneID:25574"
                     /db_xref="RGD:3927"
                     /translation="MNGEADCPTDLEMAAPKGQDRWSQEDMLTLLECMKNNLPSNDSS
                     KFKTTESHMDWEKVAFKDFSGDMCKLKWVEISNEVRKFRTLTELILDAQEHVKNPYKG
                     KKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMK
                     YIQDFQREKQEFERNLARFREDHPDLIQNAKKSDIPEKPKTPQQLWYTHEKKVYLKVR
                     PDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDYIQKHPELNISEEG
                     ITKSTLTKAERQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERMVLCSQQWKL
                     LSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEEKMLNINKKQTTSPAS
                     KKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSE
                     KKKAKYKAREAALKAQSERKPGGEREDRGKLPESPKRAEEIWQQSVIGDYLARFKNDR
                     VKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSSKKMKFQGE
                     PKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQR
                     QYKVHLDLWVKSLSPQDRAAYKEYISNKRKNMTKLRGPNPKSSRTTLQSKSESEEDDD
                     EEDDDDDDEEEEEDDENGDSSEDGGDSSESSSEDESEDGDENEDDDDDEDDDEDDDED
                     EDNESEGSSSSSSSSGDSSDSDSN"
     exon            269..444
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            445..528
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            529..684
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            685..749
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            750..870
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            871..981
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            982..1115
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            1116..1257
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            1258..1299
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            1300..1413
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            1414..1569
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            1570..1725
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            1726..1836
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            1837..1925
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            1926..2115
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            2116..2163
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            2164..2235
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            2236..2379
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
     exon            2380..4736
                     /gene="Ubtf"
                     /gene_synonym="Tcfubf"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 attagccgtc gctccgcttc gccatctcgg gctttgtctg gagactcgct gccccggcgt
       61 cggcagctgc ggagctgcgg ctcagctctt ccgcctgtgg tgctgcctgg tgcccccggc
      121 ccttactagc acccacacgc tcgggtgagg tggctttgac cccgggttgc ccggccagcg
      181 cgaccgagga ggtggctgga cagctggaga atgaacggag aagccgactg tcccacagac
      241 ctggaaatgg ccgcccccaa aggccaagac cgctggtccc aggaagatat gctaactttg
      301 ctggaatgca tgaagaacaa ccttccatcc aatgacagct ccaagttcaa gaccacagag
      361 tcgcatatgg actgggaaaa agtcgcattt aaggattttt caggagatat gtgcaagctc
      421 aaatgggtgg agatttctaa cgaggtaagg aagttccgta ctttgacaga attgatcctt
      481 gatgctcagg aacatgttaa aaacccttac aaaggcaaaa aactcaagaa acacccggat
      541 tttccaaaga aacctctcac cccctacttc cgcttcttca tggagaagcg ggccaagtac
      601 gcgaaactcc accctgagat gagcaacctg gacttgacta agatcctgtc taagaaatac
      661 aaggagcttc cagagaagaa gaagatgaaa tatattcagg acttccagag ggagaaacag
      721 gagttcgagc gaaacctggc ccgattcagg gaggatcacc ctgaccttat ccagaatgcc
      781 aagaagtcgg acatccccga gaagcccaaa actccccagc aactgtggta cacccatgag
      841 aagaaggtgt atctcaaagt gcggccggat gccactacga aggaggtgaa ggactccctg
      901 gggaagcagt ggtctcagct ctcggacaaa aagaggctga aatggattca taaggccctg
      961 gagcagcgga aggagtacga ggagattatg cgtgattata tccagaagca ccctgagcta
     1021 aacatcagcg aggaaggtat caccaagtct accctcacta aggccgaacg ccagctcaag
     1081 gacaaatttg atggacgacc caccaagcca cctccgaaca gctactccct gtactgtgca
     1141 gagctcatgg caaacatgaa ggatgtgccc agcacagagc gcatggtgct atgcagccag
     1201 cagtggaagc tgctctccca gaaggaaaag gatgcttatc acaagaagtg tgaccagaaa
     1261 aagaaagatt atgaagtgga gctgctgcgg ttccttgaga gcttgccaga ggaagagcag
     1321 cagcgggtcc tgggagagga gaagatgttg aacatcaata agaagcagac caccagtcca
     1381 gcctccaaga agccttcaca ggaaggtggc aaaggtggtt cggagaagcc caagcggcct
     1441 gtgtctgcca tgttcatctt ctcagaggag aagagaaggc agcttcagga ggaacgacct
     1501 gagctctcag aaagtgagct gacccgcctg ctggcccgca tgtggaacga cttgtccgag
     1561 aagaagaagg ctaaatataa ggcccgggag gccgcgctga aggcacagtc cgagaggaag
     1621 cctggcggag agcgtgaaga taggggcaag ttgccagagt cgcccaagag agctgaggag
     1681 atctggcagc agagtgtcat cggagactat ctggcccgct ttaagaatga ccgggtgaaa
     1741 gccttgaaag ccatggagat gacgtggaac aacatggaga agaaggagaa gctcatgtgg
     1801 attaagaagg ctgcagaaga ccaaaaacga tatgagagag agttaagtga gatgcgggcc
     1861 cctccagctg ctacgaactc ttccaagaag atgaagttcc agggagagcc caagaaaccg
     1921 cctatgaacg gttaccagaa gttctcccag gagctgctgt ccaatgggga actaaatcac
     1981 ctgccactca aggagcgcat ggtggagatc ggcagccgtt ggcagcgcat ctcccagagc
     2041 cagaaggagc actataagaa gctggctgag gaacagcaga ggcagtacaa ggtgcacttg
     2101 gacctctggg tcaagagcct atctccccag gaccgcgcag catacaaaga atacatctcc
     2161 aataaacgta agaacatgac taagcttcga ggcccaaacc ccaagtctag ccggaccacc
     2221 ctgcagtcca agtcggagtc agaggaagac gacgatgagg aagatgatga tgatgatgac
     2281 gaggaggaag aggaagatga tgagaacggc gactcgtccg aggacggtgg ggattcttct
     2341 gagtcgagca gtgaagatga aagcgaggac ggggatgaga atgaggatga tgacgacgac
     2401 gaggatgacg acgaggatga cgatgaggat gaagacaacg agtctgaggg cagtagctcc
     2461 agctcctcat cttcagggga ctcctcagat tctgactcca attgaggctc cgcctccacc
     2521 ccaggcaggc gggcaggcag gcagccaagg agagccgctg cagagcttac ctccccaact
     2581 gaccaccttt gtctccccct atgttctgtc ccctgtcccc cccagactcc cccactttct
     2641 ttctttcctt taaaaaaaaa attcagtggg gtaggaggct gcgtgagccc aggctaggac
     2701 tctgcagcct tggagcgtca gctgcagagg ttctccaggg acaacaacca tcagactgag
     2761 ccagcactgg accggcccgc cccgcccctc ttctgcactt gcagttccgg catggacagt
     2821 ggaccggaga gtttgggggt gggagcgtgt tctaaagagt ttggtgaggc cctccgagtc
     2881 tgcagcctgc cgcaaggtgg atgttcaggg gggccttccc agacgggctt gccacctgga
     2941 cccccacatt gaaccggagg gggagaaagg tgctgccttc gagaaagcag gcagcgtccg
     3001 tgtccctctt ccctgcccct gcaggaagga gctgccagga cccgttcgtg ggggaggggc
     3061 agagtgtttt ttatatatgt gtatatattt ttttttaagc tctgagctgt caacgagacg
     3121 tttcctaccg atctcggctg ccgtctctgt tgtcatttct gggagtggga gggcttgggg
     3181 tggggtggat tgagacttaa aaaatggtct tgatatgcgt aggatgtgtg tgaagcactg
     3241 tgtgtgtgtg tgtgtgtgtg tgtgtgtgtg tgtgtgtgtg tgtgtgtgtg tggcagagag
     3301 acaggacaga caaacagata cagcatgggt gcacctgtgg ataggacaga gtatatgtgt
     3361 gtgagtgtga cagacagagc atgggtgtac ctgtggatag gagagtgagt gagtgtgtgt
     3421 gtgtgtgtgt gtgtgaaaga cattcagaca gatagagcat gggtgcaccg gtggataaga
     3481 gagaaagtgt aagagagtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt
     3541 ttgtatctat cctagaaccg gcctctttga atctggaaaa agggttggta aagggggatg
     3601 ggagatgatg cccctagcag gaacaaacca aggctgcccc tccctgcaat cttccactgt
     3661 gcctgccctc tgtgtccatg gtgcagggca cagaaaccac ctgatgcttc ctatacgagt
     3721 ttgcctctgc caaggccatg tatccctaag ctgctgcagg tctgtgctgt ccagcaggaa
     3781 agtgggaggg acagaccatg gtgtgagcct taaaagcttt tctctgatcc cctgggcttc
     3841 aggatgtgtc ctgagatctt ttacctacat gttccctgcc ttgccccatg tcctctggcc
     3901 accccccacc ccccatttcc tttgatttct caggtctgct ccccctctcc tgcctccacc
     3961 cctgtaatct ggggacgggg ctgcagaaag tactttgtgc aactggtcct ctaccccttg
     4021 ttagtagctt tggaccttct agggtcagcc ccttgacttt ctaagccaag tcaccttacc
     4081 tgtggtgatt ttcattctta ctatgttggc cagatttttt tgttcatgca gttgggtttt
     4141 gtgctgcccc accttttgcc tcttgaatga aagccagggg tggaaagtag gctctccaca
     4201 gaaagcctgc agcccagctg cctgtccttg aaggcaaaga cctggactgt gtggtggaga
     4261 ttcctaaaga gaagactccc tcctatcccc tccccacccc agccacacac atacatacac
     4321 ggtccttatt ctacaattta gtaccagggt cttatgttcc cgagagggct tgcacagaga
     4381 accccaattc cttgtttgaa caccccggac tgttacactt gagtgaaatg tgttttcact
     4441 tagaaacaac tttgaacacg acatgtgttc ctcccatttc aagtattggg aaattcttac
     4501 agacaggact gggggtgggg ggtgttggtg ctgtcagagg ttgcccaggg tatatttcag
     4561 cactgggacc cttctttttc taatatttaa ggagtatttt gtaggtttca acaaccacca
     4621 cacttgaata tttgtaccgt gggagcggct taaacatgac tgtcccagat taaggccggc
     4681 cgtggaggtt ttgttttcct tttttttgta taataaagtg agaaacaaag gtttga
//
