LOCUS       NM_006590               2183 bp    mRNA    linear   PRI 12-NOV-2024
DEFINITION  Homo sapiens ubiquitin specific peptidase 39 (USP39), transcript
            variant 1, mRNA.
ACCESSION   NM_006590
VERSION     NM_006590.4
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 2183)
  AUTHORS   Lu,C., Cai,Y., Wu,S., Wang,Y., Li,J.B., Xu,G. and Ma,J.
  TITLE     Deubiquitinating enzyme USP39 promotes the growth and metastasis of
            gastric cancer cells by modulating the degradation of RNA-binding
            protein RBM39
  JOURNAL   J Biol Chem 300 (10), 107751 (2024)
   PUBMED   39260689
  REMARK    GeneRIF: Deubiquitinating enzyme USP39 promotes the growth and
            metastasis of gastric cancer cells by modulating the degradation of
            RNA-binding protein RBM39.
REFERENCE   2  (bases 1 to 2183)
  AUTHORS   Hu,Y., Wang,Y., Hu,W., Hu,C., Wang,B., Liu,C., Deng,A., Shen,B.,
            Wu,K. and Liu,Y.
  TITLE     USP39 Promotes the Viability and Migration of Head and Neck
            Squamous Cell Carcinoma Cell by Regulating STAT1
  JOURNAL   Technol Cancer Res Treat 23, 15330338241250298 (2024)
   PUBMED   38706215
  REMARK    GeneRIF: USP39 Promotes the Viability and Migration of Head and
            Neck Squamous Cell Carcinoma Cell by Regulating STAT1.
REFERENCE   3  (bases 1 to 2183)
  AUTHORS   Chen,X., Tian,L., Zhang,L., Gao,W., Yu,M., Li,Z. and Zhang,W.
  TITLE     Deubiquitinase USP39 promotes SARS-CoV-2 replication by
            deubiquitinating and stabilizing the envelope protein
  JOURNAL   Antiviral Res 221, 105790 (2024)
   PUBMED   38158131
  REMARK    GeneRIF: Deubiquitinase USP39 promotes SARS-CoV-2 replication by
            deubiquitinating and stabilizing the envelope protein.
REFERENCE   4  (bases 1 to 2183)
  AUTHORS   Yu,J., Yuan,S., Song,J. and Yu,S.
  TITLE     USP39 interacts with SIRT7 to promote cervical squamous cell
            carcinoma by modulating autophagy and oxidative stress via FOXM1
  JOURNAL   J Transl Med 21 (1), 807 (2023)
   PUBMED   37957720
  REMARK    GeneRIF: USP39 interacts with SIRT7 to promote cervical squamous
            cell carcinoma by modulating autophagy and oxidative stress via
            FOXM1.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2183)
  AUTHORS   Choi,Y., Lee,Y., Kim,J.S., Zhang,P. and Kim,J.
  TITLE     USP39-Mediated Non-Proteolytic Control of ETS2 Suppresses Nuclear
            Localization and Activity
  JOURNAL   Biomolecules 13 (10), 1475 (2023)
   PUBMED   37892157
  REMARK    GeneRIF: USP39-Mediated Non-Proteolytic Control of ETS2 Suppresses
            Nuclear Localization and Activity.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2183)
  AUTHORS   Sowa,M.E., Bennett,E.J., Gygi,S.P. and Harper,J.W.
  TITLE     Defining the human deubiquitinating enzyme interaction landscape
  JOURNAL   Cell 138 (2), 389-403 (2009)
   PUBMED   19615732
REFERENCE   7  (bases 1 to 2183)
  AUTHORS   van Leuken,R.J., Luna-Vargas,M.P., Sixma,T.K., Wolthuis,R.M. and
            Medema,R.H.
  TITLE     Usp39 is essential for mitotic spindle checkpoint integrity and
            controls mRNA-levels of aurora B
  JOURNAL   Cell Cycle 7 (17), 2710-2719 (2008)
   PUBMED   18728397
  REMARK    GeneRIF: These observations suggest Usp39 to be involved in
            splicing of Aurora B and other mRNAs that are essential for proper
            spindle checkpoint function.
REFERENCE   8  (bases 1 to 2183)
  AUTHORS   Puente,X.S., Sanchez,L.M., Overall,C.M. and Lopez-Otin,C.
  TITLE     Human and mouse proteases: a comparative genomic approach
  JOURNAL   Nat Rev Genet 4 (7), 544-558 (2003)
   PUBMED   12838346
  REMARK    Review article
REFERENCE   9  (bases 1 to 2183)
  AUTHORS   Makarova,O.V., Makarov,E.M. and Luhrmann,R.
  TITLE     The 65 and 110 kDa SR-related proteins of the U4/U6.U5 tri-snRNP
            are essential for the assembly of mature spliceosomes
  JOURNAL   EMBO J 20 (10), 2553-2563 (2001)
   PUBMED   11350945
REFERENCE   10 (bases 1 to 2183)
  AUTHORS   Lygerou,Z., Christophides,G. and Seraphin,B.
  TITLE     A novel genetic screen for snRNP assembly factors in yeast
            identifies a conserved protein, Sad1p, also required for pre-mRNA
            splicing
  JOURNAL   Mol Cell Biol 19 (3), 2008-2020 (1999)
   PUBMED   10022888
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AK289451.1 and BC001384.2.
            
            On Nov 24, 2018 this sequence version replaced NM_006590.3.
            
            Transcript Variant: This variant (1) represents the longest
            transcript. Variants 1 and 2 encode the same isoform (1).
            
            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 :: SRR1803616.260935.1,
                                           SRR1803616.57915.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000323701.11/ ENSP00000312981.6
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2011              AK289451.1         49-2059
            2012-2183           BC001384.2         1995-2166
FEATURES             Location/Qualifiers
     source          1..2183
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2p11.2"
     gene            1..2183
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /note="ubiquitin specific peptidase 39"
                     /db_xref="GeneID:10713"
                     /db_xref="HGNC:HGNC:20071"
                     /db_xref="MIM:611594"
     exon            1..278
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     CDS             11..1708
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /EC_number="3.4.19.12"
                     /note="isoform 1 is encoded by transcript variant 1; SnRNP
                     assembly defective 1 homolog; small nuclear
                     ribonucleoprotein 65kDa (U4/U6.U5); ubiquitin specific
                     protease 39; U4/U6.U5 tri-snRNP-associated protein 2;
                     U4/U6.U5 tri-snRNP-associated 65 kDa protein; SAD1
                     homolog; inactive ubiquitin-specific peptidase 39;
                     ubiquitin carboxyl-terminal hydrolase 39"
                     /codon_start=1
                     /product="ubiquitin carboxyl-terminal hydrolase 39 isoform
                     1"
                     /protein_id="NP_006581.2"
                     /db_xref="CCDS:CCDS33234.1"
                     /db_xref="GeneID:10713"
                     /db_xref="HGNC:HGNC:20071"
                     /db_xref="MIM:611594"
                     /translation="MSGRSKRESRGSTRGKRESESRGSSGRVKRERDREREPEAASSR
                     GSPVRVKREFEPASAREAPASVVPFVRVKREREVDEDSEPEREVRAKNGRVDSEDRRS
                     RHCPYLDTINRSVLDFDFEKLCSISLSHINAYACLVCGKYFQGRGLKSHAYIHSVQFS
                     HHVFLNLHTLKFYCLPDNYEIIDSSLEDITYVLKPTFTKQQIANLDKQAKLSRAYDGT
                     TYLPGIVGLNNIKANDYANAVLQALSNVPPLRNYFLEEDNYKNIKRPPGDIMFLLVQR
                     FGELMRKLWNPRNFKAHVSPHEMLQAVVLCSKKTFQITKQGDGVDFLSWFLNALHSAL
                     GGTKKKKKTIVTDVFQGSMRIFTKKLPHPDLPAEEKEQLLHNDEYQETMVESTFMYLT
                     LDLPTAPLYKDEKEQLIIPQVPLFNILAKFNGITEKEYKTYKENFLKRFQLTKLPPYL
                     IFCIKRFTKNNFFVEKNPTIVNFPITNVDLREYLSEEVQAVHKNTTYDLIANIVHDGK
                     PSEGSYRIHVLHHGTGKWYELQDLQVTDILPQMITLSEAYIQIWKRRDNDETNQQGA"
     exon            279..348
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            349..443
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            444..580
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            581..733
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            734..959
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            960..1037
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            1038..1105
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            1106..1294
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            1295..1437
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            1438..1573
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            1574..1660
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     exon            1661..2183
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2157..2162
                     /regulatory_class="polyA_signal_sequence"
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /note="hexamer: ATTAAA"
     polyA_site      2183
                     /gene="USP39"
                     /gene_synonym="65K; CGI-21; HSPC332; SAD1; SNRNP65"
                     /note="major polyA site"
ORIGIN      
        1 ggtagtggag atgtccggcc ggtctaagcg ggagtctcgc ggttccactc gcgggaagcg
       61 agagtctgag tcgcggggca gctccggtcg cgtcaagcgg gagcgagatc gggagcggga
      121 gcctgaggcg gcgagctccc ggggcagccc tgtgcgcgtg aagcgggagt tcgagccggc
      181 gagcgcgcgc gaggccccgg cttctgttgt cccgtttgtg cgggtgaagc gggagcgcga
      241 ggtcgatgag gactcggagc ctgagcggga ggtgcgagca aagaatggcc gagtggattc
      301 tgaggaccgg aggagccgcc actgcccgta cctggacacc attaacagga gtgtgctgga
      361 ctttgacttt gagaaactgt gttctatctc cctctcacac atcaatgctt atgcctgtct
      421 ggtgtgtggc aagtactttc aaggccgggg tttgaagtct cacgcctaca ttcacagtgt
      481 ccagtttagc caccatgttt tcctcaacct ccacaccctc aagttttact gccttccaga
      541 caactatgag atcatcgatt cctcattgga ggatatcacg tatgtgttga agcccacttt
      601 cacaaagcag caaattgcaa acttggacaa gcaagccaaa ttgtcccggg catatgatgg
      661 taccacttac ctgccgggta ttgtgggact gaataacata aaggccaatg attatgccaa
      721 cgctgtcctt caggctctat ctaatgttcc tcctctccgg aactactttc tggaagaaga
      781 caattataag aacatcaaac gtcctccagg ggatatcatg ttcttgttgg tccagcgttt
      841 tggagagctg atgagaaagc tctggaaccc tcgaaatttc aaggcacatg tgtctcccca
      901 tgagatgctt caggcagttg tactttgcag taagaagact tttcagatca ccaaacaagg
      961 agatggcgtt gactttctgt cttggtttct gaatgctctg cactcagctc tggggggcac
     1021 aaagaagaaa aagaagacta ttgtgactga tgttttccag gggtccatga ggatcttcac
     1081 taaaaagctt ccccatcctg atctgccagc agaagaaaaa gagcagttgc tccataatga
     1141 cgagtaccag gagacaatgg tggagtccac ttttatgtac ctgacgctgg accttcctac
     1201 tgcccccctc tacaaggacg agaaggagca gctcatcatt ccccaagtgc cactcttcaa
     1261 catcctggct aagttcaatg gcatcactga gaaggaatat aagacttaca aggagaactt
     1321 tctgaagcgc ttccagctta ccaagttgcc tccatatcta atcttttgta tcaagagatt
     1381 cactaagaac aacttctttg ttgagaagaa tccaactatt gtcaatttcc ctattacaaa
     1441 tgtggatctg agagaatact tgtctgaaga agtacaagca gtacacaaga ataccaccta
     1501 tgacctcatt gccaacatcg tgcatgacgg caagccctcc gagggctcct accggatcca
     1561 cgtgcttcat catgggacag gcaaatggta tgaattacaa gacctccagg tgactgacat
     1621 ccttccccag atgatcacac tgtcagaggc ttacattcag atttggaaga ggcgagataa
     1681 tgatgaaacc aaccagcagg gggcttgaag gaggcgtcta gggctttgct cccaagggct
     1741 gtggctgatg atggtaaata agaacacaga agctgtagct gaacacaggc tggctggtgg
     1801 gcttcctagg ccagcccagc ttgtatgggt tctggctaca ccagagcacc aagagcccac
     1861 ttgcctggga tggccccaca ctgtcactca gctgttcttt gatcattttt ttctagattg
     1921 atgctccttt ctcccatgca ttgagctccc atctagcttc agcagggcag aacccttctc
     1981 cagatgtgtg taacttatgt cttgagtatc tgggagtagt tgaagaacag ataattcctt
     2041 ccaaacatca agccttggga ttcttggagc aagcagaaag ccagtaactt cgctctgtta
     2101 gaggtggagg attttcctat ggttcccccc atttcctgat ttgtattttt agatggatta
     2161 aatagtctcc tgtttttaaa cca
//
