LOCUS       NM_026573               2367 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus UPF3 regulator of nonsense transcripts homolog B
            (yeast) (Upf3b), mRNA.
ACCESSION   NM_026573 XM_110787
VERSION     NM_026573.3
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 2367)
  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 2367)
  AUTHORS   Ma,X., Li,Y., Chengyan,C., Shen,Y., Wang,H. and Li,T.
  TITLE     Spatial expression of the nonsense-mediated mRNA decay factors
            UPF3A and UPF3B among mouse tissues
  JOURNAL   J Zhejiang Univ Sci B 24 (11), 1062-1068 (2023)
   PUBMED   37961809
  REMARK    GeneRIF: Spatial expression of the nonsense-mediated mRNA decay
            factors UPF3A and UPF3B among mouse tissues.
REFERENCE   3  (bases 1 to 2367)
  AUTHORS   Tan,K., Jones,S.H., Lake,B.B., Chousal,J.N., Shum,E.Y., Zhang,L.,
            Chen,S., Sohni,A., Pandya,S., Gallo,R.L., Zhang,K.,
            Cook-Andersen,H. and Wilkinson,M.F.
  TITLE     The role of the NMD factor UPF3B in olfactory sensory neurons
  JOURNAL   Elife 9, e57525 (2020)
   PUBMED   32773035
  REMARK    GeneRIF: The role of the NMD factor UPF3B in olfactory sensory
            neurons.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2367)
  AUTHORS   Huang,L., Shum,E.Y., Jones,S.H., Lou,C.H., Chousal,J., Kim,H.,
            Roberts,A.J., Jolly,L.A., Espinoza,J.L., Skarbrevik,D.M.,
            Phan,M.H., Cook-Andersen,H., Swerdlow,N.R., Gecz,J. and
            Wilkinson,M.F.
  TITLE     A Upf3b-mutant mouse model with behavioral and neurogenesis defects
  JOURNAL   Mol Psychiatry 23 (8), 1773-1786 (2018)
   PUBMED   28948974
  REMARK    GeneRIF: Study reports the generation and characterization of mice
            harboring a null Upf3b allele. These Upf3b-null mice exhibit
            deficits in fear-conditioned learning, but not spatial learning.
            Upf3b-null mice also have a profound defect in prepulse inhibition.
            Cortical pyramidal neurons from Upf3b-null mice display deficient
            dendritic spine maturation in vivo.
REFERENCE   5  (bases 1 to 2367)
  AUTHORS   Shum,E.Y., Jones,S.H., Shao,A., Chousal,J.N., Krause,M.D.,
            Chan,W.K., Lou,C.H., Espinoza,J.L., Song,H.W., Phan,M.H.,
            Ramaiah,M., Huang,L., McCarrey,J.R., Peterson,K.J., De Rooij,D.G.,
            Cook-Andersen,H. and Wilkinson,M.F.
  TITLE     The Antagonistic Gene Paralogs Upf3a and Upf3b Govern
            Nonsense-Mediated RNA Decay
  JOURNAL   Cell 165 (2), 382-395 (2016)
   PUBMED   27040500
  REMARK    GeneRIF: Analysis revealed that UPF3A is a broadly acting
            nonsense-mediated RNA decay inhibitor. This discovery implies that
            UPF3A and UPF3B do not primarily work in a complementary or
            redundant manner as previously supposed; instead, they oppose each
            other, allowing this paralog pair to serve as a molecular rheostat
            to modulate the level of gene expression during development.
REFERENCE   6  (bases 1 to 2367)
  AUTHORS   Karam,R., Lou,C.H., Kroeger,H., Huang,L., Lin,J.H. and
            Wilkinson,M.F.
  TITLE     The unfolded protein response is shaped by the NMD pathway
  JOURNAL   EMBO Rep 16 (5), 599-609 (2015)
   PUBMED   25807986
REFERENCE   7  (bases 1 to 2367)
  AUTHORS   Jolly,L.A., Homan,C.C., Jacob,R., Barry,S. and Gecz,J.
  TITLE     The UPF3B gene, implicated in intellectual disability, autism, ADHD
            and childhood onset schizophrenia regulates neural progenitor cell
            behaviour and neuronal outgrowth
  JOURNAL   Hum Mol Genet 22 (23), 4673-4687 (2013)
   PUBMED   23821644
  REMARK    GeneRIF: Evidence suggests Upf3b-dependent nonsense-mediated mRNA
            decay is regulated at multiple levels during development including
            regulation of expression and sub-cellular localization of Upf3b.
REFERENCE   8  (bases 1 to 2367)
  AUTHORS   Leoyklang,P., Suphapeetiporn,K., Srichomthong,C., Tongkobpetch,S.,
            Fietze,S., Dorward,H., Cullinane,A.R., Gahl,W.A., Huizing,M. and
            Shotelersuk,V.
  TITLE     Disorders with similar clinical phenotypes reveal underlying
            genetic interaction: SATB2 acts as an activator of the UPF3B gene
  JOURNAL   Hum Genet 132 (12), 1383-1393 (2013)
   PUBMED   23925499
REFERENCE   9  (bases 1 to 2367)
  AUTHORS   Huang,L., Lou,C.H., Chan,W., Shum,E.Y., Shao,A., Stone,E.,
            Karam,R., Song,H.W. and Wilkinson,M.F.
  TITLE     RNA homeostasis governed by cell type-specific and branched
            feedback loops acting on NMD
  JOURNAL   Mol Cell 43 (6), 950-961 (2011)
   PUBMED   21925383
REFERENCE   10 (bases 1 to 2367)
  AUTHORS   Ciaudo,C., Bourdet,A., Cohen-Tannoudji,M., Dietz,H.C., Rougeulle,C.
            and Avner,P.
  TITLE     Nuclear mRNA degradation pathway(s) are implicated in Xist
            regulation and X chromosome inactivation
  JOURNAL   PLoS Genet 2 (6), e94 (2006)
   PUBMED   16789828
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AK145431.1 and BC047049.1.
            
            On Sep 1, 2015 this sequence version replaced NM_026573.2.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660817.209501.1, AK145431.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164135, SAMN01164138
                                           [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
            1-2188              AK145431.1         4-2191
            2189-2367           BC047049.1         1848-2026
FEATURES             Location/Qualifiers
     source          1..2367
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="X"
                     /map="X 21.51 cM"
     gene            1..2367
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /note="UPF3 regulator of nonsense transcripts homolog B
                     (yeast)"
                     /db_xref="GeneID:68134"
                     /db_xref="MGI:MGI:1915384"
     exon            1..247
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     CDS             92..1510
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /note="hUPF3B"
                     /codon_start=1
                     /product="regulator of nonsense transcripts 3B"
                     /protein_id="NP_080849.1"
                     /db_xref="CCDS:CCDS30068.1"
                     /db_xref="GeneID:68134"
                     /db_xref="MGI:MGI:1915384"
                     /translation="MKEEKDHRPKEKRVTLFTPQGATGGCIGATAEGAKGDDRQDRNR
                     DKKEALSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFK
                     NQEDILLFRDRFDGYVFLDNKGQEYHAIVEFAPFQKAAKKKIKKRDTKVGTIEDDPEY
                     RKFLESYATDNEKMTSTPETLLEEIEAKNRELIAKRTTPLLSFLKNKQRMREEKREER
                     RRREIERKRQREEERRKWKEEEKRKRKDIEKLKKIERIPEREKIRDEPKIKLLRKPEK
                     GDEKELDKRDKTKRLDKENLNEERASGHSYTLPRRSDVELKDEKPKRLDDEGVRDYRD
                     RDRDYERDQERMIRERERLKRQEEERRRQQQKERYEKEKAFKRKEEEMKREKEALRDK
                     GKKSENTESICSLEKIEKKEEVVKRDRIRNKDRPAMQLYQPGARSRSRLCPADDSIKP
                     GDSPVDKKQESGISHRKEGGEE"
     exon            248..354
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            355..461
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            462..560
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            561..671
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            672..715
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            716..898
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            899..1059
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            1060..1360
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            1361..2344
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2316..2321
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /note="hexamer: AATAAA"
     polyA_site      2344
                     /gene="Upf3b"
                     /gene_synonym="5730594O13Rik; RENT3B; UPF3X"
                     /note="major polyA site"
ORIGIN      
        1 ggagctcctg aggtctctcc cggagagtcg taggtgcccg gcgtaacggc ttagcagctg
       61 tgccaccgct ctaaagagcg taaccgtggc catgaaggaa gaaaaagatc ataggcctaa
      121 ggagaaacga gtgaccctgt ttacgccgca gggcgccaca ggcggctgta ttggcgctac
      181 tgccgaaggc gccaaagggg acgataggca ggatcgcaac agggacaaga aagaagcttt
      241 gagcaaggtg gtaattcgaa gattacctcc cactttgacc aaggaacagc ttcaggaaca
      301 tcttcaacct atgcctgagc acgattattt tgagtttttt tctaatgata ctagccttta
      361 tcctcatatg tatgccagag catatatcaa ctttaaaaac caagaagaca ttcttttatt
      421 cagggaccga tttgatggct atgtattcct tgacaataag ggtcaagaat atcatgctat
      481 agtagaattt gcaccatttc aaaaagctgc aaaaaagaag attaagaaaa gagatacaaa
      541 agttgggact atcgaggatg atccagaata cagaaaattt ttggagagtt atgccacaga
      601 caatgagaaa atgacatcta ctccagagac attgctggag gaaattgaag ccaaaaatcg
      661 agaattaata gctaaaagga caacgcccct tttgagcttc ctgaagaaca agcaaagaat
      721 gagagaagaa aagagagaag aaaggaggag acgggaaata gagaggaaaa ggcaaagaga
      781 agaagagaga agaaaatgga aagaagagga gaaacgaaaa agaaaagata tagaaaaact
      841 aaagaagata gaaagaattc cagaaaggga gaaaataagg gatgaaccaa agattaagtt
      901 gctcaggaaa ccggaaaaag gagatgaaaa agaacttgat aaaagagaca aaaccaagag
      961 actggacaaa gaaaatctga atgaagaaag agccagtggg cacagttata ctctgcccag
     1021 gcgttctgat gtcgaactga aggatgaaaa gccaaagagg ctcgatgacg agggtgtcag
     1081 agattacaga gacagggacc gggactatga gagagatcag gagcgcatga tccgagaaag
     1141 agagaggctg aagcggcaag aagaagagcg ccggcggcag cagcagaaag aacgctatga
     1201 gaaagagaag gcttttaagc gaaaggaaga agaaatgaag agagagaaag aggcacttcg
     1261 agataaagga aagaagagtg agaatacaga atcaatatgc tcattagaaa aaattgaaaa
     1321 aaaagaggaa gtggttaaga gagaccgcat aaggaacaag gatcgtccag ccatgcagct
     1381 ttaccaacca ggagctcgaa gccgaagccg actctgtccc gccgatgaca gcatcaagcc
     1441 tggagattcc ccagtggaca aaaagcagga aagtggtatt agccatagaa aagaaggagg
     1501 agaggagtga gaagtccaaa tggtcatagg tgtcctgact gtccaggcag ccaaagagca
     1561 cgtattatgc tatccagaag tgccttcagg gcaaaggaac agagaacaag aaaaggggtc
     1621 gctgtgctgg tgggatgtac tacagaggag tgtgtctaag cagaataaga ttgcaggctc
     1681 agaaccgaag gacaatttca ttgttttctg cagtttccac aagttaattt taatgtctca
     1741 gaaaaagatg gtagcaagaa cattgcaagt gaaaaatgtc aaataagggc ttaactttgt
     1801 atgacagcta aaaagagcag gttcgaaaat caatgggtgc tcttaatcct ggcttggagc
     1861 atcttcgttt gagtggagca gaaacacact aagtttcgtt gggatctaac tattttgcat
     1921 tgttggtgtt gactgttgac tctgtagtgt aggagcaatg agcatgtaat tgtagcacaa
     1981 gtagagcgga ggatagagca aattatggct gatggaaaag atttaaatag tcacgttaca
     2041 tctatatcct gtgtctgaag ttttcataat tacagcttgt tttaattctg taaatgtagc
     2101 atcaaaaatt ccttgtaaac atctcgtttt tgcctttagc gttttttcct attactaggt
     2161 aaaatgtagc ccttggctag ttactgacaa tctagtcttt gttttatctt aggtctgatg
     2221 atttgagtgc ataccctctt ccaggaagga agctacacca ttatctgttc ctgttatggc
     2281 agctttcagt cttagcttgt ttttgtaatg ctgtcaataa atttccactt cgttccggtt
     2341 tgaaaaaaaa aaaaaaaaaa aaaaaaa
//
