LOCUS       NM_001081132            5174 bp    mRNA    linear   ROD 10-FEB-2025
DEFINITION  Mus musculus UPF2 regulator of nonsense transcripts homolog (yeast)
            (Upf2), mRNA.
ACCESSION   NM_001081132 XM_140801
VERSION     NM_001081132.1
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 5174)
  AUTHORS   Lin,L., Zhao,J., Kubota,N., Li,Z., Lam,Y.L., Nguyen,L.P., Yang,L.,
            Pokharel,S.P., Blue,S.M., Yee,B.A., Chen,R., Yeo,G.W., Chen,C.W.,
            Chen,L. and Zheng,S.
  TITLE     Epistatic interactions between NMD and TRP53 control progenitor
            cell maintenance and brain size
  JOURNAL   Neuron 112 (13), 2157-2176 (2024)
   PUBMED   38697111
REFERENCE   2  (bases 1 to 5174)
  AUTHORS   Chousal,J.N., Sohni,A., Vitting-Seerup,K., Cho,K., Kim,M., Tan,K.,
            Porse,B., Wilkinson,M.F. and Cook-Andersen,H.
  TITLE     Progression of the pluripotent epiblast depends upon the NMD factor
            UPF2
  JOURNAL   Development 149 (21) (2022)
   PUBMED   36255229
  REMARK    GeneRIF: Progression of the pluripotent epiblast depends upon the
            NMD factor UPF2.
            Erratum:[Development. 2024 Jun 15;151(12):dev203145. doi:
            10.1242/dev.203145.. PMID: 38912553]
REFERENCE   3  (bases 1 to 5174)
  AUTHORS   Terrey,M., Adamson,S.I., Chuang,J.H. and Ackerman,S.L.
  TITLE     Defects in translation-dependent quality control pathways lead to
            convergent molecular and neurodevelopmental pathology
  JOURNAL   Elife 10, e66904 (2021)
   PUBMED   33899734
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 5174)
  AUTHORS   Zhang,Y., Xie,X., Yeganeh,P.N., Lee,D.J., Valle-Garcia,D.,
            Meza-Sosa,K.F., Junqueira,C., Su,J., Luo,H.R., Hide,W. and
            Lieberman,J.
  TITLE     Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted
            gene knockdown
  JOURNAL   Proc Natl Acad Sci U S A 118 (9) (2021)
   PUBMED   33627408
  REMARK    GeneRIF: Immunotherapy for breast cancer using EpCAM aptamer
            tumor-targeted gene knockdown.
REFERENCE   5  (bases 1 to 5174)
  AUTHORS   Lin,L., Zhang,M., Stoilov,P., Chen,L. and Zheng,S.
  TITLE     Developmental Attenuation of Neuronal Apoptosis by Neural-Specific
            Splicing of Bak1 Microexon
  JOURNAL   Neuron 107 (6), 1180-1196 (2020)
   PUBMED   32710818
REFERENCE   6  (bases 1 to 5174)
  AUTHORS   Zheng,S., Gray,E.E., Chawla,G., Porse,B.T., O'Dell,T.J. and
            Black,D.L.
  TITLE     PSD-95 is post-transcriptionally repressed during early neural
            development by PTBP1 and PTBP2
  JOURNAL   Nat Neurosci 15 (3), 381-388,S1 (2012)
   PUBMED   22246437
  REMARK    Publication Status: Online-Only
REFERENCE   7  (bases 1 to 5174)
  AUTHORS   Thoren,L.A., Norgaard,G.A., Weischenfeldt,J., Waage,J.,
            Jakobsen,J.S., Damgaard,I., Bergstrom,F.C., Blom,A.M., Borup,R.,
            Bisgaard,H.C. and Porse,B.T.
  TITLE     UPF2 is a critical regulator of liver development, function and
            regeneration
  JOURNAL   PLoS One 5 (7), e11650 (2010)
   PUBMED   20657840
  REMARK    GeneRIF: Study find that loss of Upf2 during fetal liver
            development is incompatible with postnatal life due to failure of
            terminal differentiation. Moreover, deletion of Upf2 in the adult
            liver results in hepatosteatosis and disruption of liver
            homeostasis.
            Publication Status: Online-Only
REFERENCE   8  (bases 1 to 5174)
  AUTHORS   Weischenfeldt,J., Damgaard,I., Bryder,D., Theilgaard-Monch,K.,
            Thoren,L.A., Nielsen,F.C., Jacobsen,S.E., Nerlov,C. and Porse,B.T.
  TITLE     NMD is essential for hematopoietic stem and progenitor cells and
            for eliminating by-products of programmed DNA rearrangements
  JOURNAL   Genes Dev 22 (10), 1381-1396 (2008)
   PUBMED   18483223
  REMARK    GeneRIF: Hematopoietic-specific deletion of Upf2, a core NMD
            factor, led to the rapid, complete, and lasting cell-autonomous
            extinction of all hematopoietic stem and progenitor populations.
REFERENCE   9  (bases 1 to 5174)
  AUTHORS   Banihashemi,L., Wilson,G.M., Das,N. and Brewer,G.
  TITLE     Upf1/Upf2 regulation of 3' untranslated region splice variants of
            AUF1 links nonsense-mediated and A+U-rich element-mediated mRNA
            decay
  JOURNAL   Mol Cell Biol 26 (23), 8743-8754 (2006)
   PUBMED   17000771
REFERENCE   10 (bases 1 to 5174)
  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     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AL928924.12,
            CR388026.3 and AL928735.9.
            
            On Feb 6, 2007 this sequence version replaced XM_140801.7.
            
            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 :: SRR1660813.110498.1,
                                           SRR1660815.27036.1 [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, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-85                AL928924.12        165415-165499
            86-465              AL928924.12        171417-171796
            466-1245            AL928924.12        174879-175658
            1246-1406           AL928924.12        187415-187575
            1407-1601           AL928924.12        189854-190048
            1602-1751           AL928924.12        193720-193869
            1752-1855           CR388026.3         3002-3105
            1856-1941           CR388026.3         8397-8482
            1942-2050           CR388026.3         23555-23663
            2051-2164           AL928735.9         6256-6369
            2165-2281           AL928735.9         14843-14959
            2282-2467           AL928735.9         19224-19409
            2468-2671           AL928735.9         22056-22259
            2672-2947           AL928735.9         23154-23429
            2948-3131           AL928735.9         25303-25486
            3132-3271           AL928735.9         30053-30192
            3272-3373           AL928735.9         36050-36151
            3374-3472           AL928735.9         36404-36502
            3473-3640           AL928735.9         42839-43006
            3641-3782           AL928735.9         46279-46420
            3783-3903           AL928735.9         47450-47570
            3904-5174           AL928735.9         51374-52644
FEATURES             Location/Qualifiers
     source          1..5174
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 3.62 cM"
     gene            1..5174
                     /gene="Upf2"
                     /note="UPF2 regulator of nonsense transcripts homolog
                     (yeast)"
                     /db_xref="GeneID:326622"
                     /db_xref="MGI:MGI:2449307"
     exon            1..85
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            86..465
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     CDS             104..3913
                     /gene="Upf2"
                     /note="nonsense mRNA reducing factor 2; up-frameshift
                     suppressor 2 homolog"
                     /codon_start=1
                     /product="regulator of nonsense transcripts 2"
                     /protein_id="NP_001074601.1"
                     /db_xref="CCDS:CCDS38041.1"
                     /db_xref="GeneID:326622"
                     /db_xref="MGI:MGI:2449307"
                     /translation="MPAERKKSASMEEKESLLNNKEKDCSERRPVSSKEKPRDDLKVT
                     AKKEVSKVPEDKKKRLEEDKRKKEDKERKKKEEEKVKAEEELKKKEEEEKKKQEEEER
                     KKQEEQAKRQQEEAAAQLKEKEESLQLHQEAWERHQLRKELRSKNQNAPDNRPEENFF
                     SRLDSSLKKNTAFVKKLKTITEQQRDSLSHDFNGLNLSKYIAEAVASIVEAKLKLSDV
                     NCAAHLCSLFHQRYSDFAPSLLQVWKKHFEARKEEKTPNITKLRTDLRFIAELTIVGI
                     FTDKEGLSLIYEQLKSIINADRESHTHVSVVISFCRHCGDDIAGLVPRKVKSAAEKFN
                     LSFPPSEIISPEKQQPFQNLLKEYFTSLTKHLKRDHRELQNTERQNRRILHSKGELSE
                     DRHKQYEEFAMSYQKLLANSQSLADLLDENMPDLPQDKPTPEEHGPGIDIFTPGKPGE
                     YDLEGGIWEDEDARNFYENLIDLKAFVPAILFKDNEKSQNKDSNKDDSKEAKEPKDNK
                     EASSPDDLELELENLEINDDTLELEGADEAEDLTKKLLDEQEQEDEEASTGSHLKLIV
                     DAFLQQLPNCVNRDLIDKAAMDFCMNMNTKANRKKLVRALFIVPRQRLDLLPFYARLV
                     ATLHPCMSDVAEDLCSMLRGDFRFHVRKKDQINIETKNKTVRFIGELTKFKMFTKNDT
                     LHCLKMLLSDFSHHHIEMACTLLETCGRFLFRSPESHLRTSVLLEQMMRKKQAMHLDA
                     RYVTMVENAYYYCNPPPAEKTVRKKRPPLQEYVRKLLYKDLSKVTTEKVLRQMRKLPW
                     QDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLYQEDVGIHVVDGVLEDIRLGME
                     VNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDGSPSSLDPPEHL
                     FRIRLVCTILDTCGQYFDRGSSKRKLDCFLVYFQRYVWWKKSLEVWTKDHPFPIDIDY
                     MISDTLELLRPKIKLCNSLEESIRQVQDLEREFLIKLGLVNDKESKDSMTEGENLEED
                     EEEEEGGAETEEQSGNESEVNEPEEEEGSEEEEEGEEEEEENTDYLTDSNKENETDEE
                     NAEVMIKGGGLKHVPCVEDEDFIQALDKMMLENLQQRSGESVKVHQLDVAIPLHLKSQ
                     LRKGPPLGGGEGETESADTMPFVMLTRKGNKQQFKILNVPMSSQLAANHWNQQQAEQE
                     ERMRMKKLTLDINERQEQEDYQEMLQSLAQRPAPANTNRERRPRYQHPKGAPNADLIF
                     KTGGRRR"
     exon            466..1245
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            1246..1406
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            1407..1601
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            1602..1751
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            1752..1855
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            1856..1941
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            1942..2050
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            2051..2164
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            2165..2281
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            2282..2467
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            2468..2671
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            2672..2947
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            2948..3131
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            3132..3271
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            3272..3373
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            3374..3472
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            3473..3640
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            3641..3782
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            3783..3903
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     exon            3904..5174
                     /gene="Upf2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      5149..5154
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Upf2"
                     /note="hexamer: AATAAA"
     polyA_site      5169
                     /gene="Upf2"
                     /note="major polyA site"
ORIGIN      
        1 gagagcggcg gggggagggg aggggagccc gagcgctgga gttggtgctg ggaaacccgg
       61 ggctaatgtt gacaacaggc actaggttgt cctgggtcac ataatgccag ctgagcgtaa
      121 aaagtcagca agtatggaag aaaaagaatc tttactaaac aacaaggaaa aagactgcag
      181 tgagaggcgg ccagtgagca gcaaggagaa accaagggac gacctcaagg tcactgccaa
      241 gaaggaggtc agtaaggtcc cagaagacaa aaagaagaga ctggaagaag ataagagaaa
      301 aaaggaagac aaggaacgca agaaaaaaga ggaagagaag gtgaaggcag aggaagagtt
      361 aaagaagaag gaagaggaag aaaagaagaa acaggaagag gaagagagga aaaagcagga
      421 ggagcaggcc aagcggcagc aggaagaagc ggctgctcag ctgaaagaga aagaagaatc
      481 tcttcagctt catcaggagg cctgggaacg ccatcaatta cgaaaggaac ttcgtagcaa
      541 aaaccaaaat gctccagaca accgaccaga ggaaaatttc tttagccgcc tagattcgag
      601 cttaaagaaa aataccgctt ttgtcaagaa actaaaaaca attacagaac aacagagaga
      661 ctccttgtct catgatttta atggcctgaa tttaagcaaa tatattgcag aagccgtagc
      721 ttccattgtg gaggcaaaat taaaactctc tgacgtgaac tgtgctgcgc acctctgctc
      781 tctctttcac cagcggtact ctgactttgc gccctctctt cttcaggtgt ggaaaaaaca
      841 tttcgaagcg aggaaagagg agaaaacgcc taacattacc aagctaagaa ctgacttgcg
      901 tttcattgca gaattgacaa tagtgggaat tttcactgac aaggaaggtc tttccttaat
      961 ctacgaacag ctaaaaagta ttattaatgc tgatcgagaa tcccacactc atgtttctgt
     1021 ggtgattagt ttctgtcgcc attgtggaga tgacattgct ggacttgtac cgaggaaagt
     1081 aaaaagtgct gcggagaagt ttaatttgag ttttcctcct agtgagatca ttagtccgga
     1141 gaagcagcag cctttccaga atcttttaaa agagtacttt acgtctttga ccaaacacct
     1201 gaaaagggac cacagggagc tgcagaacac tgagaggcaa aacaggcgta ttctgcactc
     1261 taaaggcgag ctaagtgagg acaggcacaa gcaatatgag gagtttgcaa tgtcttacca
     1321 gaagctgctg gcgaactctc agtccttagc ggaccttttg gatgaaaata tgcccgatct
     1381 tcctcaggac aaacccacac cagaagagca tgggcccgga atcgacatat ttacacccgg
     1441 caaacctgga gagtatgact tagaaggtgg catttgggaa gatgaagacg ctcggaattt
     1501 ttatgaaaac ctcatcgatt tgaaagcatt tgttccagcc atcttgttca aagacaatga
     1561 aaaaagtcag aacaaagatt ctaacaaaga tgattccaaa gaggcaaaag aaccaaagga
     1621 taataaggag gcatcaagtc ctgatgattt ggaacttgag ttggagaatt tagaaattaa
     1681 tgatgataca ttggagttag aaggtgcaga tgaagctgaa gatcttacaa agaaacttct
     1741 tgatgaacaa gaacaagaag atgaagaagc cagcactgga tctcatctca aactcatagt
     1801 agatgctttc ctccagcagc tgcccaactg tgtcaaccga gacctaatcg acaaggcagc
     1861 catggatttt tgcatgaaca tgaacacaaa ggcaaacagg aagaagttgg tgcgggcact
     1921 cttcatagtt cctaggcaga ggttggattt gctaccattt tatgcaagat tggttgctac
     1981 cttgcacccc tgcatgtctg atgtagcaga ggatctttgt tccatgctga ggggggattt
     2041 cagatttcat gttcgaaaaa aggaccagat caacattgaa acaaagaaca aaactgtccg
     2101 ctttattgga gagctaacca agtttaagat gttcaccaaa aatgatacac tgcattgtct
     2161 aaagatgctt ctgtcagatt tctctcatca tcatattgaa atggcatgca ctctactgga
     2221 gacctgcgga agatttctct tcagatctcc agaatcacac ctgaggacca gtgtgctttt
     2281 ggagcaaatg atgagaaaga aacaagcaat gcatcttgat gcacgatatg ttacaatggt
     2341 agaaaatgca tattattact gcaacccacc gcccgccgaa aagaccgtga gaaagaaacg
     2401 ccctcctctt caggagtatg tccgcaagct tctgtacaag gatctctcta aggtcacgac
     2461 ggaaaaggtt ttgagacaga tgcgaaagtt gccctggcag gaccaagaag taaaagacta
     2521 tgttatttgt tgtatgataa acatctggaa cgtgaaatac aacagtattc actgtgtagc
     2581 caacctccta gcagggctag ttctctacca ggaggatgtt gggatccatg ttgtggatgg
     2641 cgtactcgaa gatattcgat tgggaatgga ggttaatcaa cctaaattta accagaggcg
     2701 tatcagtagt gccaagttct taggagaact ttataattac agaatggtcg aatcagctgt
     2761 tattttcaga actctttatt cttttacttc atttggtgtc aaccctgatg ggtctccaag
     2821 ttccctggac cctcctgagc atctctttag aattagacta gtatgcacta ttttggatac
     2881 ctgtggccag tactttgaca gaggttccag taaacgaaaa cttgactgct tccttgtata
     2941 ttttcagcgt tatgtttggt ggaagaaaag tttggaggtt tggacaaaag accatccatt
     3001 tcctattgat atagattaca tgatcagtga tacactagaa ctgctaagac caaagatcaa
     3061 actctgtaat tctctggaag aatccatcag gcaggtacaa gacttggaac gagaattctt
     3121 aataaaacta ggcctagtaa atgacaaaga gtccaaagat tctatgacag aaggggaaaa
     3181 tcttgaagag gatgaagaag aagaagaagg aggagctgag acagaggaac agtctggaaa
     3241 tgaaagtgaa gtgaacgagc cagaagaaga agagggttct gaggaggagg aggagggaga
     3301 ggaggaggaa gaggagaata cagattacct cacagattcc aacaaggaga acgagactga
     3361 tgaagaaaat gctgaggtga tgattaaggg aggcggactg aagcatgttc cttgtgtaga
     3421 agatgaggac ttcattcaag ctctggacaa aatgatgcta gaaaaccttc agcagcgaag
     3481 tggtgagtct gttaaagtgc accagcttga tgttgctatc cctttgcatc tcaaaagcca
     3541 gctgaggaaa gggcccccgc ttggcggtgg ggaaggagag acggagtctg cagacacgat
     3601 gccatttgtc atgttaacaa gaaaaggcaa taaacagcag tttaagattc tcaatgtgcc
     3661 catgtcatcc caacttgctg caaatcattg gaaccagcaa caagcagaac aagaggagag
     3721 gatgaggatg aaaaagctca ccttagacat caatgaacga caagagcaag aagattatca
     3781 agaaatgttg cagtctcttg cacagcgccc agctccagca aacactaatc gtgagcggcg
     3841 gcctcgttac cagcatccaa agggagcacc taatgcagat ctaatcttta agactggtgg
     3901 gaggagacgt tgatccagca gcacgtgtca tttcattagg tcctgtatct gatgttgtgg
     3961 atagtggagt cctccagcaa ttgaatgaga gcagcggaca catctcagca tgtcggtcta
     4021 gagagttgcg aatctaaacc tgggacaggc tggggccatg aggcagaaac accagcctct
     4081 gccaacaccg gaacaagccg acgcttccag acaaggcaga aaggcctttt gtaatggaaa
     4141 tcacgtgagg gttaatcttc tcttgagaat ggcagtcaag aaatgagaag gtgcacttga
     4201 ctactgagca gttacaccaa gaagagcgtc cacgaggtga ctgagccgga gaagaaacag
     4261 ttgagatggg aatggtatgg gggaaatgaa cttgagtttt aaacttgatt taagttacag
     4321 tgtctctgaa tcgaacatcc catgttggaa gaagatacac ttgggggctc caggactaca
     4381 gtagaaaagt atagagcaag cagtaaaatc ttctagtaaa aacatacatg caggacaaca
     4441 aaatgatgaa agagatccaa atgccagata agccaccagg aaaggtgttg ttaaggagtt
     4501 tgtttcaaga ggagcaaggg atgagggaga aaaacctgtg ttaaccatca gagtcagtga
     4561 tgtaaagttg cctattagag tgaaagaaac tgtgaagact gttaatatgc aaagcattaa
     4621 tgcagatggt ttagaaggtc tgataccagc ctaagaacgg ggatatagtt gagcccattg
     4681 taagtatcat tgaaaacaaa cggtgccagt gagcatgtca cagaagaacg aaggacagca
     4741 agaagcggat cagagtattt tgttgacctt catgggttta cagcctctgt gtctaaacaa
     4801 gatatggaaa caagtagagc ttttactttg cttttgtttt cgtttcgttt tgttcccctt
     4861 tccccactag aaatgagggt tcttagtctg tttctgacag tctgttaatt tattaggata
     4921 ggtgtctttc atttgctttc cagtaggcat agtgatttag ttaaagaaca catctgtatg
     4981 ctacaacttg atcacatctt ttttctattt tgcatctttc ttttaccatg tttcagtttc
     5041 tgcatgtaga tttcaataag aaacaaaact tgtaaagttg taacatttca catggaaatg
     5101 ctgcccaatc ttcaccagct tcagaaatct gacctttgcc gatgctgcaa taaagtgttg
     5161 taatttggat ttgg
//
