LOCUS       NM_023011               2370 bp    mRNA    linear   PRI 01-JUN-2024
DEFINITION  Homo sapiens UPF3A regulator of nonsense mediated mRNA decay
            (UPF3A), transcript variant 1, mRNA.
ACCESSION   NM_023011
VERSION     NM_023011.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2370)
  AUTHORS   Xu,W., Ou,W., Feng,Y., Xu,Q., Yang,Y., Cui,L. and Du,P.
  TITLE     Genetic compensation response could exist in colorectal cancer:
            UPF3A upregulates the oncogenic homologue gene SRSF3 expression
            corresponding to SRSF6 to promote colorectal cancer metastasis
  JOURNAL   J Gastroenterol Hepatol 38 (4), 634-647 (2023)
   PUBMED   36807382
  REMARK    GeneRIF: Genetic compensation response could exist in colorectal
            cancer: UPF3A upregulates the oncogenic homologue gene SRSF3
            expression corresponding to SRSF6 to promote colorectal cancer
            metastasis.
REFERENCE   2  (bases 1 to 2370)
  AUTHORS   Bufton,J.C., Powers,K.T., Szeto,J.A., Toelzer,C., Berger,I. and
            Schaffitzel,C.
  TITLE     Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A
            in complex with UPF2 reveal molecular basis for competitive binding
            and for neurodevelopmental disorder-causing mutation
  JOURNAL   Nucleic Acids Res 50 (10), 5934-5947 (2022)
   PUBMED   35640974
  REMARK    GeneRIF: Structures of nonsense-mediated mRNA decay factors UPF3B
            and UPF3A in complex with UPF2 reveal molecular basis for
            competitive binding and for neurodevelopmental disorder-causing
            mutation.
REFERENCE   3  (bases 1 to 2370)
  AUTHORS   Yi,Z., Arvola,R.M., Myers,S., Dilsavor,C.N., Abu Alhasan,R.,
            Carter,B.N., Patton,R.D., Bundschuh,R. and Singh,G.
  TITLE     Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay
            independently of their exon junction complex binding
  JOURNAL   EMBO J 41 (10), e109202 (2022)
   PUBMED   35451102
  REMARK    GeneRIF: Mammalian UPF3A and UPF3B can activate nonsense-mediated
            mRNA decay independently of their exon junction complex binding.
REFERENCE   4  (bases 1 to 2370)
  AUTHORS   Wallmeroth,D., Lackmann,J.W., Kueckelmann,S., Altmuller,J.,
            Dieterich,C., Boehm,V. and Gehring,N.H.
  TITLE     Human UPF3A and UPF3B enable fault-tolerant activation of
            nonsense-mediated mRNA decay
  JOURNAL   EMBO J 41 (10), e109191 (2022)
   PUBMED   35451084
  REMARK    GeneRIF: Human UPF3A and UPF3B enable fault-tolerant activation of
            nonsense-mediated mRNA decay.
REFERENCE   5  (bases 1 to 2370)
  AUTHORS   Michalak,M., Katzenmaier,E.M., Roeckel,N., Woerner,S.M., Fuchs,V.,
            Warnken,U., Yuan,Y.P., Bork,P., Neu-Yilik,G., Kulozik,A., von
            Knebel Doeberitz,M., Kloor,M., Kopitz,J. and Gebert,J.
  TITLE     (Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells
            Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism
            Caused by Frameshift Mutation of NMD Regulator UPF3A
  JOURNAL   Int J Mol Sci 21 (15), 5234 (2020)
   PUBMED   32718059
  REMARK    GeneRIF: (Phospho)proteomic Profiling of Microsatellite Unstable
            CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol
            Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2370)
  AUTHORS   Lykke-Andersen,J., Shu,M.D. and Steitz,J.A.
  TITLE     Communication of the position of exon-exon junctions to the mRNA
            surveillance machinery by the protein RNPS1
  JOURNAL   Science 293 (5536), 1836-1839 (2001)
   PUBMED   11546874
REFERENCE   7  (bases 1 to 2370)
  AUTHORS   Kim,V.N., Kataoka,N. and Dreyfuss,G.
  TITLE     Role of the nonsense-mediated decay factor hUpf3 in the
            splicing-dependent exon-exon junction complex
  JOURNAL   Science 293 (5536), 1832-1836 (2001)
   PUBMED   11546873
  REMARK    GeneRIF: binds to spliced mRNAs upstream of exon-exon junctions; is
            part of mRNP complexes that are ready for nuclear export and that
            participate in nonsense-mediated mRNA decay
REFERENCE   8  (bases 1 to 2370)
  AUTHORS   Yamashita,A., Ohnishi,T., Kashima,I., Taya,Y. and Ohno,S.
  TITLE     Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein
            kinase, associates with components of the mRNA surveillance complex
            and is involved in the regulation of nonsense-mediated mRNA decay
  JOURNAL   Genes Dev 15 (17), 2215-2228 (2001)
   PUBMED   11544179
REFERENCE   9  (bases 1 to 2370)
  AUTHORS   Serin,G., Gersappe,A., Black,J.D., Aronoff,R. and Maquat,L.E.
  TITLE     Identification and characterization of human orthologues to
            Saccharomyces cerevisiae Upf2 protein and Upf3 protein
            (Caenorhabditis elegans SMG-4)
  JOURNAL   Mol Cell Biol 21 (1), 209-223 (2001)
   PUBMED   11113196
REFERENCE   10 (bases 1 to 2370)
  AUTHORS   Lykke-Andersen,J., Shu,M.D. and Steitz,J.A.
  TITLE     Human Upf proteins target an mRNA for nonsense-mediated decay when
            bound downstream of a termination codon
  JOURNAL   Cell 103 (7), 1121-1131 (2000)
   PUBMED   11163187
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AY013250.1, BC008694.1 and
            BQ008047.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_023011.3.
            
            Summary: This gene encodes a protein that is part of a
            post-splicing multiprotein complex involved in both mRNA nuclear
            export and mRNA surveillance. The encoded protein is one of two
            functional homologs to yeast Upf3p. mRNA surveillance detects
            exported mRNAs with truncated open reading frames and initiates
            nonsense-mediated mRNA decay (NMD). When translation ends upstream
            from the last exon-exon junction, this triggers NMD to degrade
            mRNAs containing premature stop codons. This protein binds to the
            mRNA and remains bound after nuclear export, acting as a
            nucleocytoplasmic shuttling protein. It forms with Y14 a complex
            that binds specifically 20 nt upstream of exon-exon junctions. This
            gene is located on the long arm of chromosome 13. Several splice
            variants encoding different isoforms have been found for this gene.
            [provided by RefSeq, Jul 2017].
            
            Transcript Variant: This variant (1) encodes the longest isoform
            (Upf3p).
            
            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 :: SRR1803613.93868.1,
                                           SRR1660805.74853.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000375299.8/ ENSP00000364448.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1646              AY013250.1         18-1663
            1647-2361           BC008694.1         1077-1791
            2362-2370           BQ008047.1         16-24               c
FEATURES             Location/Qualifiers
     source          1..2370
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="13"
                     /map="13q34"
     gene            1..2370
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /note="UPF3A regulator of nonsense mediated mRNA decay"
                     /db_xref="GeneID:65110"
                     /db_xref="HGNC:HGNC:20332"
                     /db_xref="MIM:605530"
     exon            1..246
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     CDS             40..1470
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /note="isoform hUpf3p is encoded by transcript variant 1;
                     nonsense mRNA reducing factor 3A; up-frameshift suppressor
                     3 homolog A; UPF3 regulator of nonsense transcripts
                     homolog A"
                     /codon_start=1
                     /product="regulator of nonsense transcripts 3A isoform
                     hUpf3p"
                     /protein_id="NP_075387.1"
                     /db_xref="CCDS:CCDS9543.1"
                     /db_xref="GeneID:65110"
                     /db_xref="HGNC:HGNC:20332"
                     /db_xref="MIM:605530"
                     /translation="MRSEKEGAGGLRAAVAARGPSGREKLSALEVQFHRDSQQQEAET
                     PPTSSSGCGGGAGKPREEKRTALSKVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAA
                     DLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAVVEFAPFQKIAKKK
                     LRKKDAKTGSIEDDPEYKKFLETYCVEEEKTSANPETLLGEMEAKTRELIARRTTPLL
                     EYIKNRKLEKQRIREEKREERRRRELEKKRLREEEKRRRREEERCKKKETDKQKKIAE
                     KEVRIKLLKKPEKGEEPTTEKPKERGEEIDTGGGKQESCAPGAVVKARPMEGSLEEPQ
                     ETSHSGSDKEHRDVERSQEQESEAQRYHVDDGRRHRAHHEPERLSRRSEDEQRWGKGP
                     GQDRGKKGSQDSGAPGEAMERLGRAQRCDDSPAPRKERLANKDRPALQLYDPGARFRA
                     RECGGNRRICKAEGSGTGPEKREEAE"
     exon            247..353
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     exon            354..460
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     exon            461..559
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     exon            560..670
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     exon            671..726
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     exon            727..885
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     exon            886..1046
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     exon            1047..1341
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     exon            1342..2370
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2341..2346
                     /regulatory_class="polyA_signal_sequence"
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /note="hexamer: AATAAA"
     polyA_site      2370
                     /gene="UPF3A"
                     /gene_synonym="HUPF3A; RENT3A; UPF3"
                     /note="major polyA site"
ORIGIN      
        1 gtcgggggct ggcggctgcg gctcggcgga gagtgcggca tgcgctcgga aaaggagggg
       61 gccggaggcc ttcgggcggc cgttgccgcg cggggcccga gcgggaggga gaagctgtcg
      121 gccctagaag tgcagttcca ccgcgactcg cagcagcagg aggctgagac gccgccaact
      181 tcgtcctccg gttgcggggg cggtgcgggc aaacctcgcg aggagaagag gacggccctg
      241 agcaaggtgg tcatccgccg cctgcctccg ggcctcacca aggagcagct ggaggagcag
      301 ctgcgcccgc tgccagcaca cgactacttc gagttcttcg ccgccgacct gagtctttat
      361 cctcatctct actcaagagc atacattaat tttaggaatc ctgatgacat ccttcttttt
      421 agagatcgtt ttgatggata tatcttcctt gacagcaaag gcctagaata tcctgcagtg
      481 gtagagtttg ctccattcca gaagatagcc aaaaagaagc tgagaaaaaa agatgccaag
      541 actggaagca tcgaagatga tccagaatat aagaagtttt tagaaaccta ctgtgtggag
      601 gaagagaaga ccagtgccaa ccctgagact ctgctggggg agatggaggc gaagacaaga
      661 gagctcattg ctagaagaac cacacctctt ttggaatata ttaaaaatag aaaattagaa
      721 aagcagagaa ttcgagaaga gaagcgagaa gaacggagga ggagagagtt agaaaagaaa
      781 cgtttgcggg aagaggaaaa aagaagaaga agagaagaag aaagatgcaa aaaaaaagag
      841 acagataaac agaagaaaat tgcagagaaa gaagtaagga ttaagcttct taagaaacca
      901 gaaaagggag aggaaccaac cacagagaaa ccaaaagaaa gaggagagga gattgatact
      961 ggaggtggca agcaggaatc ctgtgccccc ggtgcagtcg taaaagccag gcccatggaa
     1021 ggctcgctgg aggagcccca ggagacgtca cacagcggca gtgataaaga gcacagggat
     1081 gtggagagat ctcaagaaca agaatctgaa gcacaaagat accatgtgga tgacggcagg
     1141 aggcacagag ctcaccacga gcctgaacgg ctttccagaa ggagtgagga tgagcagaga
     1201 tgggggaaag gacctggcca agacagaggg aagaagggga gccaggacag cggggctccg
     1261 ggggaggcca tggagagact gggaagagcg cagaggtgtg acgacagtcc agcacccaga
     1321 aaagagcgac tggcaaacaa ggaccggcca gccttgcagc tgtatgatcc aggagctcgc
     1381 ttccgagcgc gagagtgtgg cggaaacagg aggatctgca aggcagaagg ttcggggact
     1441 ggtcctgaga agagggaaga ggcagagtga gtcactgcac gcacctggcc tccatggacg
     1501 agcaagggca tcccagaaac gtgtaaatga ccccgagtgt gactgggaag gagaacttat
     1561 tccttaccag gaaactggaa gctaaaaata cagagggtga cgtagaaaca cgcagaaacc
     1621 attctaaaga aagtagtgat cttgtattaa attgagcaga attctcacag attttaccat
     1681 tcctgttata aactagtatt tgttgtttag ccaaaacaga aaatgatttc cactggacag
     1741 tagaaaaata tgtgtaaaat agggaagaaa gttagtattg gatcagtgtg agtcctgaag
     1801 cactttcagt gctgtgagaa cgacatccac tttgggtttc attcgtttgt aagcagagga
     1861 gctgtcagtc actcgtgctt ctcggtggcc tctgagccat ggtgtcgagt gaagagtagt
     1921 tcttgtttgt tacaaccttt gtgagtcagc catgcccgca aagcgtgctg tgttttagtc
     1981 ctggtaggaa tatttatcag agttcacact atataaaacc caacagcttc aactattgcc
     2041 ctttcaacag ttttgccact gaccggatag aaacggtttc agtctctgga tggatgtgtt
     2101 tgtggtttgt aaccattacg gtttaaacca tggtttaaga atttgcccaa ataacagaaa
     2161 ttttgttcgg gaagggataa actagatata gcatacagag cctgtttttg agttttagat
     2221 actttatttg taaataactt aaaatagctt tctgaaaccg tgcattctgt agtttcttcc
     2281 tttcagtgaa attgctaaat gtcaatgtat ttttggcact gcgattttaa ccatttatta
     2341 aataaaaatt ttgttaaaga agtactgaaa
//
