LOCUS       NM_001198573            5303 bp    mRNA    linear   ROD 14-JUN-2024
DEFINITION  Mus musculus ubiquitin specific peptidase 40 (Usp40), transcript
            variant 1, mRNA.
ACCESSION   NM_001198573
VERSION     NM_001198573.2
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 5303)
  AUTHORS   Miao,J., Li,L., Shaheen,N., Wei,J., Jacko,A.M., Sundd,P.,
            Taleb,S.J., Mallampalli,R.K., Zhao,Y. and Zhao,J.
  TITLE     The deubiquitinase USP40 preserves endothelial integrity by
            targeting the heat shock protein HSP90beta
  JOURNAL   Exp Mol Med 56 (2), 395-407 (2024)
   PUBMED   38307937
  REMARK    GeneRIF: The deubiquitinase USP40 preserves endothelial integrity
            by targeting the heat shock protein HSP90beta.
REFERENCE   2  (bases 1 to 5303)
  AUTHORS   Takahashi,S., Fukuhara,D., Kimura,T., Fukutomi,T., Tanaka,E.,
            Mikami,N., Hada,I., Takematsu,H., Nishibori,Y., Akimoto,Y.,
            Kiyonari,H., Abe,T., Huber,O. and Yan,K.
  TITLE     USP40 deubiquitinates HINT1 and stabilizes p53 in podocyte damage
  JOURNAL   Biochem Biophys Res Commun 614, 198-206 (2022)
   PUBMED   35605301
  REMARK    GeneRIF: USP40 deubiquitinates HINT1 and stabilizes p53 in podocyte
            damage.
REFERENCE   3  (bases 1 to 5303)
  AUTHORS   Pang,A.L., Taylor,H.C., Johnson,W., Alexander,S., Chen,Y., Su,Y.A.,
            Li,X., Ravindranath,N., Dym,M., Rennert,O.M. and Chan,W.Y.
  TITLE     Identification of differentially expressed genes in mouse
            spermatogenesis
  JOURNAL   J Androl 24 (6), 899-911 (2003)
   PUBMED   14581517
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC087801.69 and AC162281.3.
            
            On Jan 12, 2023 this sequence version replaced NM_001198573.1.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC117958.1, SRR10223970.657.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-99                AC087801.69        171911-172009
            100-317             AC087801.69        173005-173222
            318-385             AC162281.3         307-374
            386-499             AC162281.3         2099-2212
            500-664             AC162281.3         4717-4881
            665-811             AC162281.3         6662-6808
            812-955             AC162281.3         8767-8910
            956-1084            AC162281.3         10319-10447
            1085-1180           AC162281.3         14464-14559
            1181-1288           AC162281.3         15629-15736
            1289-1586           AC162281.3         18422-18719
            1587-1668           AC162281.3         20786-20867
            1669-1840           AC162281.3         22441-22612
            1841-1925           AC162281.3         23566-23650
            1926-1996           AC162281.3         24536-24606
            1997-2319           AC162281.3         25988-26310
            2320-2443           AC162281.3         28690-28813
            2444-2501           AC162281.3         30487-30544
            2502-2555           AC162281.3         36172-36225
            2556-2644           AC162281.3         37023-37111
            2645-2731           AC162281.3         37351-37437
            2732-2768           AC162281.3         39279-39315
            2769-2833           AC162281.3         42133-42197
            2834-2908           AC162281.3         44758-44832
            2909-3032           AC162281.3         47287-47410
            3033-3127           AC162281.3         50376-50470
            3128-3246           AC162281.3         52163-52281
            3247-3312           AC162281.3         52913-52978
            3313-3523           AC162281.3         54252-54462
            3524-3619           AC162281.3         54594-54689
            3620-3714           AC162281.3         56025-56119
            3715-5303           AC162281.3         57914-59502
FEATURES             Location/Qualifiers
     source          1..5303
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="1"
                     /map="1 44.45 cM"
     gene            1..5303
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /note="ubiquitin specific peptidase 40"
                     /db_xref="GeneID:227334"
                     /db_xref="MGI:MGI:2443184"
     exon            1..99
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            100..317
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     CDS             119..3826
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /EC_number="3.4.19.12"
                     /note="isoform 1 is encoded by transcript variant 1;
                     ubiquitin specific protease 40; ubiquitin
                     carboxyl-terminal hydrolase 40; ubiquitin thioesterase 40;
                     deubiquitinating enzyme 40; ubiquitin-specific-processing
                     protease 40; ubiquitin thiolesterase 40"
                     /codon_start=1
                     /product="ubiquitin carboxyl-terminal hydrolase 40 isoform
                     1"
                     /protein_id="NP_001185502.1"
                     /db_xref="CCDS:CCDS78645.1"
                     /db_xref="GeneID:227334"
                     /db_xref="MGI:MGI:2443184"
                     /translation="MFGNLFEEDYSSVSSSQYGRGKKLKTKGLEPPAPREFTNLSGIR
                     NQGGTCYLSSLLQTLHFTPEFREALFSLGPEELGSLEDKDKPDAKVRIIPLQLQRLFA
                     QLLLLDQEAASTIDLTDSFGWTNDEEMRQHDVQELNRILFSALETSLVGTSGHDLIHR
                     LYHGTIVNQIVCKECKNISERQEDFLDLTVAVKNVSGLEDELCNMYVEEEIFDYDNLY
                     HCGTCDRLVKAAKSAKLRKLPPFLTISLLRFNFDFVKCERYKDTSCYTFPLRINLKPF
                     CEQSELDDMEYMYDLFSVIIHKGGCYGGHYHVYIKDVDHLGNWQCQEEISDTNVNVKA
                     PQSEEEANDPLVVLKTILLQEEANQIPVDQLGQKLLKKTGISWNKKYRKQHGPLRKFL
                     QLHPQIFLLSTDESTVSLLRNHLTQAPSDLQSCEQILHTLASESPGLNDDTSCPHWFD
                     INDSKVHPIREKDITQQFQGKESAYMLFYRKATLQRPPEARANPRYRVPCHLLKEMDA
                     ANILLQMRRAECDSANSTFELHLHLGPHYRFFNGALHPAVSETESVWDLTFDKRKTLG
                     DLRQSIFQLLECWEGDMVLSVAKRVPAGLHVYHTLDGDDLTLCEAEVADGEDIFVWNG
                     VEVGGVQIQTGFDCEPLLLNILHLELSGEGSKCEQLVESPHVFPANAEVGAVFTALGT
                     PAGAILMNSVESADGECWTAVPKEDMKKTFREQGLRNGSLILVQDSDSDNNSLLPKQG
                     RWTNSMNELNWLQVKNFCQSESEEKQVQIAVTMHTVVFDIRIKAIKELKLMKELAENS
                     CLRPIDRNGKLLCPVPDSSTLEEAEVKMGSSVGLCLGKAPTSSQLFLFFALGTDIHPG
                     AEMDIIVEETLSVRDCLKIMLEKSGQQGEIWHLRKMDWCYEAGEPLCEEDATLKELMI
                     RSGDTLLLTEGKLPPPGHLKMPIWWYQPARLSGHCESRDHLNCAFSQDSTWRAAPTQG
                     APGPEPAEVSLLYLGDMEISEEATLVELKSQALALPSVSKLAVQSTALLRVWTVESKR
                     PSRLLRTNWRQLKEYRLGRRAELCLELLQKEEDLGPRDVLLRTQLRIPGERAYSLATD
                     LIWDTTRGWTAGSLRQRVADFYSLPVEKIEIAKYFPEKFEWLPISSWNQQVAKRKKKK
                     NQDTLQGGPYYLKDGDTIGIKNLLFDDNDDFSTIRDDIGKENQKRLALEKKKSREVHR
                     AQSSDLFSNAGVPARFRGPEASLSIHVASFR"
     exon            318..385
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            386..499
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            500..664
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            665..811
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            812..955
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            956..1084
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            1085..1180
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            1181..1288
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            1289..1586
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            1587..1668
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            1669..1840
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            1841..1925
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            1926..1996
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            1997..2319
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2320..2443
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2444..2501
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2502..2555
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2556..2644
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2645..2731
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2732..2768
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2769..2833
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2834..2908
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            2909..3032
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            3033..3127
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            3128..3246
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            3247..3312
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            3313..3523
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            3524..3619
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            3620..3714
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     exon            3715..5303
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /inference="alignment:Splign:2.1.0"
     regulatory      5273..5278
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /note="hexamer: AATAAA"
     polyA_site      5303
                     /gene="Usp40"
                     /gene_synonym="B230215L03Rik; C730029K03"
                     /note="major polyA site"
ORIGIN      
        1 actttccaga gacacggcct cctcggcatg gcggtgcccg ttcggagcga gttcgtttac
       61 tctgtgctgt ggccggggcg ggggtctggg ctataggcag atagcgttta gttccaccat
      121 gtttgggaac ctatttgaag aggattattc cagtgtgtca agtagtcagt atggaagagg
      181 gaagaaatta aagactaaag gtttggagcc gcctgcccct agagaattca ccaatttaag
      241 tggaatcaga aatcagggtg gaacctgtta cctcagctcc cttcttcaga cgcttcattt
      301 cacacctgaa ttcagagaag ctttattttc tcttggtccg gaagagctgg gttctttaga
      361 ggataaagat aaacctgatg caaaggttcg gatcatacct ttgcagttgc agcgcttgtt
      421 tgcccagctt ctgctcttgg accaggaggc tgcatctacc atagacctca ccgacagctt
      481 cgggtggacc aacgatgagg aaatgaggca acatgatgtg caggaactca accgaattct
      541 cttcagtgct ttggaaactt ctttagttgg gacctctggc catgacctca ttcatcgtct
      601 ataccatggc accattgtga accagattgt ttgcaaagag tgtaagaaca tcagtgagag
      661 gcaggaagac ttcttggatt tgacagtagc agtcaaaaat gtatctggtt tagaagatga
      721 actctgcaac atgtatgtgg aggaagaaat ttttgactat gacaacctgt accactgtgg
      781 aacctgtgac cgactggtta aagcagcaaa gtctgccaaa ttgcgtaagc tgcctccttt
      841 tcttactatt tcattactaa gatttaattt tgattttgtg aaatgtgaac gctacaagga
      901 tactagctgt tatacattcc ccctccggat caatctcaag cctttctgtg aacagagtga
      961 actggatgac atggaatata tgtatgacct cttctccgtc attatccaca aaggtggctg
     1021 ctatggaggt cattaccatg tgtacattaa agatgttgat catcttggca actggcaatg
     1081 tcaagaggag ataagtgata caaatgtgaa tgtgaaagct cctcagagtg aagaagaggc
     1141 taatgatcca ttggtggttc taaaaacaat cttattgcag gaggaggcca atcaaattcc
     1201 tgttgatcaa ctgggccaga aactcttgaa aaaaacagga atatcttgga acaagaagta
     1261 caggaaacag catggaccac tgcgaaagtt cttacagctc catcctcaga tatttctgct
     1321 cagcacagat gaaagtacag ttagtctcct gaggaaccat cttacccagg ccccatctga
     1381 cctacagagc tgtgaacaga ttctacatac acttgcttca gaatccccag gcttgaatga
     1441 tgacaccagt tgcccacact ggtttgatat caatgattcc aaagtccatc caatcagaga
     1501 gaaagatatc acacagcagt tccagggtaa agaaagtgcc tacatgctgt tttatcggaa
     1561 agccacgtta caaaggcccc ctgaagctcg agccaatcca agatacagag ttccatgtca
     1621 cttgctgaag gaaatggatg cagccaacat tctactgcag atgagaaggg cagaatgtga
     1681 ctctgcaaac agtacttttg agttgcatct tcatttgggt cctcactacc gtttcttcaa
     1741 tggggctctt caccctgcag tctctgagac agaaagcgtg tgggacttaa cgtttgataa
     1801 aagaaaaact ttaggagatc tccgtcagtc aatatttcag ctattggaat gttgggaagg
     1861 agacatggtt cttagtgttg cgaagcgtgt gccagcagga cttcatgtgt accacaccct
     1921 cgatggagat gacttgacac tgtgtgaagc tgaggttgct gatggggaag acatctttgt
     1981 atggaatggg gtagaggttg gtggagtcca aattcagact ggttttgatt gtgaacctct
     2041 gctgttaaac attcttcatc tagaactaag tggtgaaggc tcaaaatgtg agcagttggt
     2101 ggagtcacca catgtctttc ctgctaatgc agaagtgggc gctgtgttca cagccttggg
     2161 caccccagca ggtgccatcc tcatgaacag tgtggagtct gcagatggag agtgctggac
     2221 tgctgttccc aaagaagaca tgaagaagac gttcagagaa caaggtctca gaaatggaag
     2281 cttaattttg gttcaagatt cagacagtga taataacagt ctgttgccca aacaagggag
     2341 atggaccaac agcatgaatg agctcaactg gctccaagtg aaaaatttct gccagtcaga
     2401 atctgaagag aagcaggttc agatagccgt gaccatgcac acagtggtgt ttgatattcg
     2461 aattaaagcc ataaaggaat taaaattaat gaaggaacta gctgagaaca gctgtttgag
     2521 acccattgat agaaacggga agcttctttg tccagtccca gacagtagca ctttggagga
     2581 agcagaggtg aagatgggga gctccgtggg cctgtgtctg ggaaaagcac caacttcctc
     2641 tcagctgttc ctgttttttg ctctggggac tgacattcac cctggggcag agatggacat
     2701 catagtagaa gaaacactct cagtgagaga ttgtttaaag ataatgctgg agaagtcagg
     2761 tcagcaagga gagatttggc acttaaggaa aatggattgg tgctatgaag ctggtgaacc
     2821 tttatgtgaa gaggatgcaa cactgaaaga gcttatgata cgttctgggg atactttgct
     2881 tttaactgaa gggaaacttc ctcctccggg tcacttgaag atgcccatct ggtggtacca
     2941 gcctgcaagg ctgtcaggac actgtgagag tcgggaccac ttaaactgtg ccttttctca
     3001 agatagcacc tggagggctg ctcccaccca aggtgctcct ggccccgagc ctgcagaagt
     3061 ctctctcctc tacttggggg atatggagat ctcagaagag gccacattgg tggaactgaa
     3121 gtctcaggcc ttggccttgc cttctgtttc gaagctcgct gtccagtcca cagccctgct
     3181 cagagtctgg acagtggaga gcaagcgccc cagcagactc ttgcgcacta actggcggca
     3241 gctcaaggag tacagactgg gccggagagc agagctctgc ctagagctcc ttcaaaaaga
     3301 ggaggacttg gggccccgag atgtactgct gaggacacag ctacgcatcc ctggtgagag
     3361 agcctactcc ctggcgacag acctgatatg ggacaccacc agaggatgga ctgctggctc
     3421 cttgaggcag agagtagctg acttctattc tcttcctgtg gagaaaattg aaattgccaa
     3481 atattttcct gaaaagtttg agtggcttcc aatatctagc tggaatcagc aagttgccaa
     3541 aagaaaaaag aagaaaaacc aagatacttt gcaaggggga ccatattact tgaaagatgg
     3601 agacactatt ggcattaaga atctcctgtt tgatgacaat gatgatttca gcacaatcag
     3661 agatgacatt ggaaaggaga accagaagcg gctagctttg gaaaaaaaga aaagccgaga
     3721 agtccaccgt gcacagagca gcgatttgtt ctccaatgca ggggtgcccg ctaggttccg
     3781 gggaccagaa gcttctctgt ccatccacgt tgcaagcttc agatagcccc tgcagcagta
     3841 tttcctgtgc ttcagacaga agcatcctgt cagttctatg acagacacct tgtgggttta
     3901 tggtggacaa gctggttgcc tccacagcta gtgatctcaa gtcttcagct ttgtgatagg
     3961 cgaagggatg gcacttctca gaccaaacaa gtgtgcctgg ttactagctc tgtgacacag
     4021 cagctgcaga gccggctcag actcagacac tatgcccgga atagacctct tacctgtggc
     4081 ctctttccag aaagtatact tctggacaat ggcaagttgc tcaaagagga caaatctgat
     4141 aggtaagcca caagatcagt tacttaccca ctcctgaggt gaccagttag tcatctagtt
     4201 ctggcacctt actgaagctg caaggaagga tgtgtgtcct gactccattc ccagttttcc
     4261 agtcctcact atgccatgtg cctcctcttg agccaaattc aaagtaggac tctaagccag
     4321 cttgcaggaa aagctatgta tggcattcac ctactgtgtt atctaccacc tatgcactct
     4381 ggccagagac gggaccatca aagaagccta gcacaacaaa tccaggctcc catttgtctt
     4441 ggggaaactg aggcctcctc cttctcagtc agcacaggta actgattgaa gagatttggt
     4501 atttatgtac tgtaattaat acactatcaa aacagcatct attactgaac tagcaggttt
     4561 aggaccctgg gctgacttag cctatgacag acagtattcc taagaggaat tgtcagggta
     4621 tcagtttctt accagctttt acatgtcttc ctgtaacaga actgatgtgg tgtaagacaa
     4681 agaaaaagtt actctggcct gggcttcagc tagcccctgc tggcttttca catttctggt
     4741 gcagctatgc tggcttctct gtggagctga tgctcagctg gtaatcttgc tcttcctttg
     4801 tcttcccaac atcatttgcc agagttgatg tcatgttagg tgactgattc tattgaagca
     4861 cttgtattat aagatgttgg acttggacta gttacctttt ctggccatgt ccttgtagct
     4921 acacaccaag aggttctggg agacccaaac agtaaacatt acttgaccac aactgagccc
     4981 tctggatact ggatactgtt tcttgtactg taactgacat ggttccttag tttgtcccca
     5041 ggcaatacag tcctgatgta ctagctcaga cactttgctt tcaggaagcc agaggctccc
     5101 tgaccctctt agtacctgga ggagccagaa gacatgcctc aagtgctagc tgcagcctaa
     5161 gtctgttgac aggcctatct ggttggtttc ttttgtgtgt gtgtgtgtgt gtgtgtttgg
     5221 agaacagaat agacaaaaca gggaaaaaca ctaagacttt attaaagaaa aaaataaaac
     5281 attcttaaag ttgcagtcct caa
//
