LOCUS       NM_080632               2343 bp    mRNA    linear   PRI 03-OCT-2024
DEFINITION  Homo sapiens UPF3B regulator of nonsense mediated mRNA decay
            (UPF3B), transcript variant 1, mRNA.
ACCESSION   NM_080632
VERSION     NM_080632.3
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 2343)
  AUTHORS   Hou,B., Shu,M., Liu,C., Du,Y., Xu,C., Jiang,H., Hou,J., Chen,X.,
            Wang,L. and Wu,X.
  TITLE     Unveiling the role of UPF3B in hepatocellular carcinoma: Potential
            therapeutic target
  JOURNAL   Cancer Sci 115 (8), 2646-2658 (2024)
   PUBMED   38889220
  REMARK    GeneRIF: Unveiling the role of UPF3B in hepatocellular carcinoma:
            Potential therapeutic target.
REFERENCE   2  (bases 1 to 2343)
  AUTHORS   Buchwald,G., Ebert,J., Basquin,C., Sauliere,J., Jayachandran,U.,
            Bono,F., Le Hir,H. and Conti,E.
  TITLE     Insights into the recruitment of the NMD machinery from the crystal
            structure of a core EJC-UPF3b complex
  JOURNAL   Proc Natl Acad Sci U S A 107 (22), 10050-10055 (2010)
   PUBMED   20479275
  REMARK    GeneRIF: 3.4 A resolution crystal structure of a minimal UPF3b-EJC
            assembly, consisting of the interacting domains of five proteins
            (UPF3b, MAGO, Y14, eIF4AIII, and Barentsz) together with RNA and
            adenylyl-imidodiphosphate
REFERENCE   3  (bases 1 to 2343)
  AUTHORS   Chan,W.K., Bhalla,A.D., Le Hir,H., Nguyen,L.S., Huang,L., Gecz,J.
            and Wilkinson,M.F.
  TITLE     A UPF3-mediated regulatory switch that maintains RNA surveillance
  JOURNAL   Nat Struct Mol Biol 16 (7), 747-753 (2009)
   PUBMED   19503078
  REMARK    GeneRIF: Results suggest that UPF3A levels are tightly regulated by
            a post-transcriptional switch to maintain appropriate levels of NMD
            substrates in cells containing different levels of UPF3B.
REFERENCE   4  (bases 1 to 2343)
  AUTHORS   Lejeune,F., Ranganathan,A.C. and Maquat,L.E.
  TITLE     eIF4G is required for the pioneer round of translation in mammalian
            cells
  JOURNAL   Nat Struct Mol Biol 11 (10), 992-1000 (2004)
   PUBMED   15361857
REFERENCE   5  (bases 1 to 2343)
  AUTHORS   Lu,S. and Cullen,B.R.
  TITLE     Nonsense mediated decay induced by tethered human UPF3B is
            restricted to the cytoplasm
  JOURNAL   RNA Biol 1 (1), 42-47 (2004)
   PUBMED   17194930
  REMARK    GeneRIF: UPF3B induces nonsense mediated decay in the cytoplasm
REFERENCE   6  (bases 1 to 2343)
  AUTHORS   Lykke-Andersen,J.
  TITLE     Identification of a human decapping complex associated with hUpf
            proteins in nonsense-mediated decay
  JOURNAL   Mol Cell Biol 22 (23), 8114-8121 (2002)
   PUBMED   12417715
REFERENCE   7  (bases 1 to 2343)
  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
  REMARK    GeneRIF: binds RNPS1 protein, part of the postsplicing complex
            deposited 5' to exon-exon junctions
REFERENCE   8  (bases 1 to 2343)
  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   9  (bases 1 to 2343)
  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 2343)
  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 BC121017.1, AF318576.1 and
            AA657616.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Oct 30, 2019 this sequence version replaced NM_080632.2.
            
            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 X. Two splice
            variants encoding different isoforms have been found for this gene.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) encodes the longer protein
            (isoform 1), also known as hUpf3-X.
            
            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 :: AF318576.1, SRR14038194.3636891.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000276201.7/ ENSP00000276201.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-36                BC121017.1         9-44
            37-2336             AF318576.1         22-2321
            2337-2343           AA657616.1         302-308
FEATURES             Location/Qualifiers
     source          1..2343
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xq24"
     gene            1..2343
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /note="UPF3B regulator of nonsense mediated mRNA decay"
                     /db_xref="GeneID:65109"
                     /db_xref="HGNC:HGNC:20439"
                     /db_xref="MIM:300298"
     exon            1..191
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     CDS             36..1487
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /note="isoform 1 is encoded by transcript variant 1;
                     regulator of nonsense transcripts 3B; nonsense mRNA
                     reducing factor 3B; up-frameshift suppressor 3 homolog B;
                     up-frameshift suppressor 3 homolog on chromosome X; UPF3
                     regulator of nonsense transcripts homolog B"
                     /codon_start=1
                     /product="regulator of nonsense transcripts 3B isoform 1"
                     /protein_id="NP_542199.1"
                     /db_xref="CCDS:CCDS14588.1"
                     /db_xref="GeneID:65109"
                     /db_xref="HGNC:HGNC:20439"
                     /db_xref="MIM:300298"
                     /translation="MKEEKEHRPKEKRVTLLTPAGATGSGGGTSGDSSKGEDKQDRNK
                     EKKEALSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFK
                     NQEDIILFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPEY
                     RKFLESYATDNEKMTSTPETLLEEIEAKNRELIAKKTTPLLSFLKNKQRMREEKREER
                     RRREIERKRQREEERRKWKEEEKRKRKDIEKLKKIDRIPERDKLKDEPKIKVHRFLLQ
                     AVNQKNLLKKPEKGDEKELDKREKAKKLDKENLSDERASGQSCTLPKRSDSELKDEKP
                     KRPEDESGRDYREREREYERDQERILRERERLKRQEEERRRQKERYEKEKTFKRKEEE
                     MKKEKDTLRDKGKKAESTESIGSSEKTEKKEEVVKRDRIRNKDRPAMQLYQPGARSRN
                     RLCPPDDSTKSGDSAAERKQESGISHRKEGGEE"
     exon            192..298
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            299..405
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            406..504
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            505..615
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            616..659
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            660..842
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            843..881
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            882..1042
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            1043..1337
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     exon            1338..2343
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2315..2320
                     /regulatory_class="polyA_signal_sequence"
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /note="hexamer: AATAAA"
     polyA_site      2343
                     /gene="UPF3B"
                     /gene_synonym="HUPF3B; MRX62; MRX82; MRXS14; RENT3B;
                     UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X; UPF3X"
                     /note="major polyA site"
ORIGIN      
        1 gttccggcca agccgcttca gcgggggacg tagccatgaa ggaagagaag gagcacaggc
       61 ctaaggagaa gcgagtaacc ctgttaaccc ccgccggggc cacaggcagc ggtggtggga
      121 cctcggggga cagctccaag ggggaagata agcaggatcg caacaaggag aagaaagaag
      181 cgctgagcaa ggtggtaatt cgaagattac ctcccacttt gaccaaggag cagcttcagg
      241 aacatcttca acctatgcct gagcatgatt attttgagtt tttttctaat gatacgagtt
      301 tgtatcctca tatgtatgcc agagcataca tcaactttaa aaaccaagag gacattattt
      361 tgttcaggga tcgctttgat ggttatgtat tccttgacaa taaaggtcag gaatatcccg
      421 ctatagtaga atttgcacct tttcaaaaag ctgcaaaaaa gaagactaag aaaagagata
      481 ccaaagtcgg gactatcgat gatgatccag aatatagaaa gtttttggaa agttatgcca
      541 cagataatga gaaaatgaca tctactccag agacactgct agaggaaata gaagcaaaaa
      601 atagagaatt aatagctaaa aagacaaccc cacttttgag cttcctgaaa aacaagcaga
      661 gaatgagaga agaaaagaga gaagaaagga ggaggagaga aatagaaaga aaaagacaaa
      721 gagaagaaga gaggaggaaa tggaaagaag aagagaaacg aaaaaggaaa gatatagaaa
      781 agctaaagaa gatagacaga attccagaaa gggacaaatt aaaggatgaa ccaaagatta
      841 aggtacacag gtttctgtta caagctgtga atcagaaaaa tctgctcaag aagccagaaa
      901 aaggagatga aaaagaattg gacaaaagag aaaaagccaa gaaattggac aaagagaatc
      961 tcagtgatga aagagccagt gggcaaagtt gtacattgcc caagcgttct gatagcgaac
     1021 ttaaagatga aaaaccaaag agacctgaag atgagagcgg cagagactat agggagaggg
     1081 aacgggaata tgaacgagat caggagcgca tacttcgaga aagagagagg ctgaagcggc
     1141 aagaagaaga gcgccgtagg cagaaggagc gctatgagaa agagaagact tttaagagaa
     1201 aagaagaaga aatgaaaaaa gagaaagaca cacttcggga taaaggaaag aaggctgaaa
     1261 gtacagaatc aataggcagc tcagaaaaaa ctgaaaagaa agaagaagtg gtcaagagag
     1321 atcgaataag aaacaaggat cgtccagcga tgcagcttta ccaaccagga gctcgaagcc
     1381 gaaatcgact ctgtccccct gatgacagca ccaagtctgg agattcagca gcagaaagga
     1441 agcaggaaag tggtattagc catagaaaag aaggaggaga ggagtgataa gtccagatgg
     1501 ccttaggtgt cctgactgtc taggcagcca aagagcacac gttaagcaat ccagaggtgc
     1561 cttcagggca aagaatagag agaaagggag ccgctgtgct ggtggggtac actgcagagg
     1621 agtaagtctt gtgtcaaagc aggaatctga tcagaggttc agaattggaa gtacaatttc
     1681 attgcttttg caatttctac aaattaattt taaagtgtca gaaaaaggtg acggcaagga
     1741 catgcattgc aatttgcagg gggaattgtc aagtgaggac ttcatcacat atgacacgag
     1801 agaaaagtaa gagctggttc taaaatcaaa agctgttgtt catcctgaat tgaattttct
     1861 gaatttgggt ggagcagagt cgctttgaag ccttgttccg atctaattct attgtattgt
     1921 tgatgataag tgttgacatt gggtagtgta gaagcaacaa gcatgtcctt gtagtacagg
     1981 tacagtgaag gatagaacac actttcgttg atacaaaaat ttaaatagtt atgttacttc
     2041 tgtatccagt gtcctaaagt tttaggatta gttttagttt tttgtttgct tatatgagct
     2101 tagcgtaaag aatattttta aacttcgtgt tttgtcatca gcatcttttc tattaagagg
     2161 taaaatgtag tccttgtttg actcttgaca atccagtgtg tttgatctta ggtctcatga
     2221 tctgagtgca taccctctcc aggaaggaaa ctgcaccagt gtctattcct gttaaatagc
     2281 aacttttagt ctcagcttgt ttcgttttga tgtcaataaa tagtaacagc attcaagtgt
     2341 gaa
//
