LOCUS       NM_138592               2132 bp    mRNA    linear   ROD 24-OCT-2024
DEFINITION  Mus musculus ubiquitin specific peptidase 39 (Usp39), transcript
            variant 1, mRNA.
ACCESSION   NM_138592
VERSION     NM_138592.5
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 2132)
  AUTHORS   Ding,R., Yu,X., Hu,Z., Dong,Y., Huang,H., Zhang,Y., Han,Q.,
            Ni,Z.Y., Zhao,R., Ye,Y. and Zou,Q.
  TITLE     Lactate modulates RNA splicing to promote CTLA-4 expression in
            tumor-infiltrating regulatory T cells
  JOURNAL   Immunity 57 (3), 528-540 (2024)
   PUBMED   38417442
REFERENCE   2  (bases 1 to 2132)
  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   3  (bases 1 to 2132)
  AUTHORS   Cui,D., Wang,Z., Dang,Q., Wang,J., Qin,J., Song,J., Zhai,X.,
            Zhou,Y., Zhao,L., Lu,G., Liu,H., Liu,G., Liu,R., Shao,C., Zhang,X.
            and Liu,Z.
  TITLE     Spliceosome component Usp39 contributes to hepatic lipid
            homeostasis through the regulation of autophagy
  JOURNAL   Nat Commun 14 (1), 7032 (2023)
   PUBMED   37923718
  REMARK    GeneRIF: Spliceosome component Usp39 contributes to hepatic lipid
            homeostasis through the regulation of autophagy.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2132)
  AUTHORS   Zheng,J., Wu,S., Tang,M., Xi,S., Wang,Y., Ren,J., Luo,H., Hu,P.,
            Sun,L., Du,Y., Yang,H., Wang,F., Gao,H., Dai,Z., Ou,X. and Li,Y.
  TITLE     USP39 promotes hepatocellular carcinogenesis through regulating
            alternative splicing in cooperation with SRSF6/HNRNPC
  JOURNAL   Cell Death Dis 14 (10), 670 (2023)
   PUBMED   37821439
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2132)
  AUTHORS   Quan,J., Zhao,X., Xiao,Y., Wu,H., Di,Q., Wu,Z., Chen,X., Tang,H.,
            Zhao,J., Guan,Y., Xu,Y. and Chen,W.
  TITLE     USP39 Regulates NF-kappaB-Mediated Inflammatory Responses through
            Deubiquitinating K48-Linked IkappaBalpha
  JOURNAL   J Immunol 210 (5), 640-652 (2023)
   PUBMED   36651806
  REMARK    GeneRIF: USP39 Regulates NF-kappaB-Mediated Inflammatory Responses
            through Deubiquitinating K48-Linked IkappaBalpha.
REFERENCE   6  (bases 1 to 2132)
  AUTHORS   Yoshikawa,T., Piao,Y., Zhong,J., Matoba,R., Carter,M.G., Wang,Y.,
            Goldberg,I. and Ko,M.S.
  TITLE     High-throughput screen for genes predominantly expressed in the ICM
            of mouse blastocysts by whole mount in situ hybridization
  JOURNAL   Gene Expr Patterns 6 (2), 213-224 (2006)
   PUBMED   16325481
REFERENCE   7  (bases 1 to 2132)
  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
REFERENCE   8  (bases 1 to 2132)
  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   9  (bases 1 to 2132)
  AUTHORS   Ko,M.S., Threat,T.A., Wang,X., Horton,J.H., Cui,Y., Wang,X.,
            Pryor,E., Paris,J., Wells-Smith,J., Kitchen,J.R., Rowe,L.B.,
            Eppig,J., Satoh,T., Brant,L., Fujiwara,H., Yotsumoto,S. and
            Nakashima,H.
  TITLE     Genome-wide mapping of unselected transcripts from extraembryonic
            tissue of 7.5-day mouse embryos reveals enrichment in the t-complex
            and under-representation on the X chromosome
  JOURNAL   Hum Mol Genet 7 (12), 1967-1978 (1998)
   PUBMED   9811942
REFERENCE   10 (bases 1 to 2132)
  AUTHORS   Lesh,J.S., Burrows,H.L., Seasholtz,A.F. and Camper,S.A.
  TITLE     Mapping of the mouse corticotropin-releasing hormone receptor 2
            gene (Crhr2) to chromosome 6
  JOURNAL   Mamm Genome 8 (12), 944-945 (1997)
   PUBMED   9383293
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC116115.11.
            
            On Aug 13, 2022 this sequence version replaced NM_138592.4.
            
            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 :: BC026983.1, AK045062.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-279               AC116115.11        108973-109251       c
            280-349             AC116115.11        106987-107056       c
            350-444             AC116115.11        104055-104149       c
            445-581             AC116115.11        102481-102617       c
            582-734             AC116115.11        101790-101942       c
            735-960             AC116115.11        100348-100573       c
            961-1038            AC116115.11        97198-97275         c
            1039-1106           AC116115.11        93538-93605         c
            1107-1295           AC116115.11        92606-92794         c
            1296-1438           AC116115.11        89734-89876         c
            1439-1574           AC116115.11        85344-85479         c
            1575-1661           AC116115.11        83828-83914         c
            1662-2132           AC116115.11        82857-83327         c
FEATURES             Location/Qualifiers
     source          1..2132
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="6"
                     /map="6 32.27 cM"
     gene            1..2132
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /note="ubiquitin specific peptidase 39"
                     /db_xref="GeneID:28035"
                     /db_xref="MGI:MGI:107622"
     exon            1..279
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     CDS             15..1709
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /EC_number="3.4.19.12"
                     /note="isoform 1 is encoded by transcript variant 1; SnRNP
                     assembly defective 1 homolog; ubiquitin specific protease
                     39; U4/U6.U5 tri-snRNP-associated protein 2; inactive
                     ubiquitin-specific peptidase 39; U4/U6.U5
                     tri-snRNP-associated 65 kDa protein; ubiquitin
                     carboxyl-terminal hydrolase 39"
                     /codon_start=1
                     /product="ubiquitin carboxyl-terminal hydrolase 39 isoform
                     1"
                     /protein_id="NP_613058.1"
                     /db_xref="CCDS:CCDS20238.1"
                     /db_xref="GeneID:28035"
                     /db_xref="MGI:MGI:107622"
                     /translation="MSSRSKRQSHGSTRGKRESESRGSSGRIKKERDREKEPEAASSR
                     GSPVRVKREAEPAAREVPAPALPVVRVKREREADEDSEPEREVRAKNGRVDSEDRRSR
                     HCPYLDTINRSVLDFDFEKLCSISLSHINAYACLVCGKYFQGRGLKSHAYIHSVQFSH
                     HVFLNLHTLKFYCLPDNYEIIDSSLEDITYVLKPTFTKQQIANLDKQAKLSRAYDGTT
                     YLPGIVGLNNIKANDYANAVLQALSNVPPLRNYFLEEDNYKNIKRPPGDIMFLLVQRF
                     GELMRKLWNPRNFKAHVSPHEMLQAVVLCSKKTFQITKQGDGVDFLSWFLNALHSALG
                     GTKKKKKTIVNDVFQGSMRIFTKKLPHPDLPAEEKEQLLHNDEYQETMVESTFMYLTL
                     DLPTAPLYKDEKEQLIIPQVPLFNILAKFNGITEKEYKTYKENFLKRFQLTKLPPYLI
                     FCIKRFTKNNFFVEKNPTIVNFPITNVDLREYLSEEVQAVHKNTTYDLIANIVHDGKP
                     SEGSYRIHVLHHGTGKWYELQDLQVTDILPQMITLSEAYIQIWKRRDNDETNQQGA"
     exon            280..349
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            350..444
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            445..581
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            582..734
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            735..960
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            961..1038
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1039..1106
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1107..1295
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1296..1438
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1439..1574
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1575..1661
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            1662..2132
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2109..2114
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /note="hexamer: ATTAAA"
     polyA_site      2132
                     /gene="Usp39"
                     /gene_synonym="CGI-21; D6Wsu157e; SAD1"
                     /note="major polyA site"
ORIGIN      
        1 aactggtggt ggcgatgtct agccggtcca agcggcagtc ccatggttcc acccgcggga
       61 agcgtgagtc cgagtctcgt ggcagctcgg gtcgcatcaa gaaggagcga gaccgtgaga
      121 aggagcccga ggcggcgagc tcccggggta gcccggtccg cgtgaagcgg gaggccgagc
      181 cggctgcgcg agaggtcccg gcgcccgcgc tcccggtcgt gcgggtgaag cgtgagcgcg
      241 aggccgatga agactcggag cccgagcggg aggtgcgagc aaagaatggc cgagtggatt
      301 ctgaagaccg gaggagtcgt cactgcccgt acttggatac cattaatagg agtgtgctgg
      361 acttcgactt tgagaaactc tgctccattt ctctctcgca catcaacgca tacgcctgtc
      421 tggtgtgtgg caagtacttt caaggccggg gcttaaagtc tcatgcctac atccacagtg
      481 tccagttcag ccaccatgtc ttcctcaacc tccacactct caagttttac tgccttcctg
      541 acaactatga aatcattgat tcctcgctgg aggatatcac gtatgtgttg aagcctactt
      601 tcacaaagca gcaaattgca aacttggata agcaagccaa attgtcccgg gcatatgatg
      661 gcaccactta cctgccaggg atcgtgggac tgaacaacat aaaagccaac gactatgcaa
      721 atgctgtgct gcaggctcta tctaatgtcc ctcctcttcg gaactacttc ctggaggaag
      781 acaattacaa gaacatcaag cgtcctccgg gggacatcat gttcttgttg gttcagcgtt
      841 ttggagagct gatgagaaag ctctggaacc cccgaaactt caaggcgcat gtctctcctc
      901 atgagatgct tcaggctgtc gtactttgca gcaagaagac tttccaaatt accaaacaag
      961 gggatggagt tgacttcctg tcttggtttc tgaatgctct gcactctgct ctgggaggca
     1021 ccaagaagaa gaaaaagact attgtgaatg atgttttcca gggatcaatg agaattttca
     1081 ccaaaaagct tcctcatcct gatctgccag cggaagagaa agagcagctg ctccacaatg
     1141 atgagtacca agagacgatg gtagagtcca cgttcatgta cctgacgctg gaccttccca
     1201 cggccccgct ctataaggat gagaaggagc agctcatcat cccccaggtg cctctcttca
     1261 acatcctggc caagttcaac ggcatcacgg agaaggaata caagacttat aaggagaact
     1321 tcctgaaacg cttccagctc accaagctgc ctccgtatct aatcttttgc atcaagagat
     1381 ttactaagaa caacttcttt gtggagaaga atccaacaat tgtcaacttc cctatcacaa
     1441 atgtggatct gagagaatac ttatctgaag aagtccaagc cgtccacaag aacaccacct
     1501 atgatctcat cgccaacatc gtgcatgatg gcaagccctc tgagggctcc tacaggatcc
     1561 acgtgcttca tcatgggact ggcaagtggt atgaattaca agacctccag gtgacagaca
     1621 ttctgcccca gatgatcaca ctgtctgagg cgtacattca gatttggaag aggcgggaca
     1681 atgatgaaac caaccagcag ggggcttgaa cgccttgttg ggtttttatt cccaagggct
     1741 gtggctgaag atggtaaata aaaatactga agctgtcgct gaacacagac tgactgaaag
     1801 attcctgccc cagtccagtt tttatggatt ctggctgcat caccatgaag gagcctgtct
     1861 gccctgatgt tctgcgctgt ctccggcagc acgttgtggt cgacactctt ccctttcagc
     1921 atcagcaggc agaactctta cagatggatg ccttatttga attgctgcaa gtatcaaaga
     1981 acagacagtt cggtagaaac gtcaggtctg gagaccctag gagtaaacgt gaagtcagca
     2041 gcagccttct gtcataggta gtggctttcc tgtagctccc ttcatctcct gtgggacgtg
     2101 tgcgatggat taaatatcct cctgttttta aa
//
