LOCUS       NM_018566               6396 bp    mRNA    linear   PRI 07-MAR-2025
DEFINITION  Homo sapiens YOD1 deubiquitinase (YOD1), transcript variant 1,
            mRNA.
ACCESSION   NM_018566 XR_000127
VERSION     NM_018566.4
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 6396)
  AUTHORS   Liu,C., Fan,C., Liu,J., Zhang,S., Tang,H., Liu,Y., Zhang,S., Wu,Q.,
            Zhang,J., Qi,Z. and Shen,Y.
  TITLE     YOD1 protects against MRSA sepsis-induced DIC through Lys33-linked
            deubiquitination of NLRP3
  JOURNAL   Cell Death Dis 15 (5), 360 (2024)
   PUBMED   38789414
  REMARK    GeneRIF: YOD1 protects against MRSA sepsis-induced DIC through
            Lys33-linked deubiquitination of NLRP3.
            Erratum:[Cell Death Dis. 2024 Sep 4;15(9):651. doi:
            10.1038/s41419-024-06991-1. PMID: 39231970]
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6396)
  AUTHORS   Han,Z., Jia,Q., Zhang,J., Chen,M., Wang,L., Tong,K., He,W.,
            Zhang,Y., Zhu,W., Qin,J., Wang,T., Liu,T., Ma,Y., Chen,Y., Zha,S.
            and Zhang,C.
  TITLE     Deubiquitylase YOD1 regulates CDK1 stability and drives
            triple-negative breast cancer tumorigenesis
  JOURNAL   J Exp Clin Cancer Res 42 (1), 228 (2023)
   PUBMED   37667382
  REMARK    GeneRIF: Deubiquitylase YOD1 regulates CDK1 stability and drives
            triple-negative breast cancer tumorigenesis.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 6396)
  AUTHORS   Yin,Q., Shen,X., Xu,H., Feng,W., Shi,X. and Ju,S.
  TITLE     YY1-induced LncRNA-TUG1 elevates YOD1 to promote cell proliferation
            and inhibit bortezomib sensitivity in multiple myeloma
  JOURNAL   Leuk Lymphoma 64 (6), 1161-1174 (2023)
   PUBMED   37078241
  REMARK    GeneRIF: YY1-induced LncRNA-TUG1 elevates YOD1 to promote cell
            proliferation and inhibit bortezomib sensitivity in multiple
            myeloma.
REFERENCE   4  (bases 1 to 6396)
  AUTHORS   Park,S.S., Do,H.A., Park,H.B., Choi,H.S. and Baek,K.H.
  TITLE     Deubiquitinating enzyme YOD1 deubiquitinates and destabilizes
            alpha-synuclein
  JOURNAL   Biochem Biophys Res Commun 645, 124-131 (2023)
   PUBMED   36682332
  REMARK    GeneRIF: Deubiquitinating enzyme YOD1 deubiquitinates and
            destabilizes alpha-synuclein.
REFERENCE   5  (bases 1 to 6396)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   6  (bases 1 to 6396)
  AUTHORS   Wang,L.Q., Zhang,Y., Yan,H., Liu,K.J. and Zhang,S.
  TITLE     MicroRNA-373 functions as an oncogene and targets YOD1 gene in
            cervical cancer
  JOURNAL   Biochem Biophys Res Commun 459 (3), 515-520 (2015)
   PUBMED   25747718
  REMARK    GeneRIF: miR-373 increases proliferation by directly targeting YOD1
            in cervical cancer.
REFERENCE   7  (bases 1 to 6396)
  AUTHORS   Bernardi,K.M., Williams,J.M., Inoue,T., Schultz,A. and Tsai,B.
  TITLE     A deubiquitinase negatively regulates retro-translocation of
            nonubiquitinated substrates
  JOURNAL   Mol Biol Cell 24 (22), 3545-3556 (2013)
   PUBMED   24068323
REFERENCE   8  (bases 1 to 6396)
  AUTHORS   Mevissen,T.E., Hospenthal,M.K., Geurink,P.P., Elliott,P.R.,
            Akutsu,M., Arnaudo,N., Ekkebus,R., Kulathu,Y., Wauer,T., El
            Oualid,F., Freund,S.M., Ovaa,H. and Komander,D.
  TITLE     OTU deubiquitinases reveal mechanisms of linkage specificity and
            enable ubiquitin chain restriction analysis
  JOURNAL   Cell 154 (1), 169-184 (2013)
   PUBMED   23827681
REFERENCE   9  (bases 1 to 6396)
  AUTHORS   Shin,J.H., Ko,H.S., Kang,H., Lee,Y., Lee,Y.I., Pletinkova,O.,
            Troconso,J.C., Dawson,V.L. and Dawson,T.M.
  TITLE     PARIS (ZNF746) repression of PGC-1alpha contributes to
            neurodegeneration in Parkinson's disease
  JOURNAL   Cell 144 (5), 689-702 (2011)
   PUBMED   21376232
REFERENCE   10 (bases 1 to 6396)
  AUTHORS   Ernst,R., Mueller,B., Ploegh,H.L. and Schlieker,C.
  TITLE     The otubain YOD1 is a deubiquitinating enzyme that associates with
            p97 to facilitate protein dislocation from the ER
  JOURNAL   Mol Cell 36 (1), 28-38 (2009)
   PUBMED   19818707
  REMARK    GeneRIF: The assignment of a p97-associated ubiquitin processing
            function to YOD1 adds to our understanding of p97's role in the
            dislocation of misfolded proteins from the endoplasmic reticulum.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL445493.8.
            
            On Jul 24, 2020 this sequence version replaced NM_018566.3.
            
            Summary: Protein ubiquitination controls many intracellular
            processes, including cell cycle progression, transcriptional
            activation, and signal transduction. This dynamic process,
            involving ubiquitin conjugating enzymes and deubiquitinating
            enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are
            cysteine proteases that specifically cleave ubiquitin from
            ubiquitin-conjugated protein substrates. The protein encoded by
            this gene belongs to a DUB subfamily characterized by an ovarian
            tumor (OTU) domain. Alternative splicing results in multiple
            transcript variants. [provided by RefSeq, Jan 2013].
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (1).
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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 :: BC137166.1, AL833081.2 [ECO:0000332]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000315927.9/ ENSP00000326813.4
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-521               AL445493.8         10158-10678         c
            522-6396            AL445493.8         3319-9193           c
FEATURES             Location/Qualifiers
     source          1..6396
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q32.1"
     gene            1..6396
                     /gene="YOD1"
                     /gene_synonym="DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907"
                     /note="YOD1 deubiquitinase"
                     /db_xref="GeneID:55432"
                     /db_xref="HGNC:HGNC:25035"
                     /db_xref="MIM:612023"
     exon            1..521
                     /gene="YOD1"
                     /gene_synonym="DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907"
                     /inference="alignment:Splign:2.1.0"
     CDS             179..1225
                     /gene="YOD1"
                     /gene_synonym="DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907"
                     /EC_number="3.4.19.12"
                     /note="isoform 1 is encoded by transcript variant 1; YOD1
                     OTU deubiquinating enzyme 1 homolog (yeast); OTU domain
                     containing 2; ubiquitin thioesterase OTU1; hsHIN7;
                     HIV-1-induced protease 7; OTU domain-containing protein 2"
                     /codon_start=1
                     /product="ubiquitin thioesterase OTU1 isoform 1"
                     /protein_id="NP_061036.3"
                     /db_xref="CCDS:CCDS31002.1"
                     /db_xref="GeneID:55432"
                     /db_xref="HGNC:HGNC:25035"
                     /db_xref="MIM:612023"
                     /translation="MFGPAKGRHFGVHPAPGFPGGVSQQAAGTKAGPAGAWPVGSRTD
                     TMWRLRCKAKDGTHVLQGLSSRTRVRELQGQIAAITGIAPGGQRILVGYPPECLDLSN
                     GDTILEDLPIQSGDMLIIEEDQTRPRSSPAFTKRGASSYVRETLPVLTRTVVPADNSC
                     LFTSVYYVVEGGVLNPACAPEMRRLIAQIVASDPDFYSEAILGKTNQEYCDWIKRDDT
                     WGGAIEISILSKFYQCEICVVDTQTVRIDRFGEDAGYTKRVLLIYDGIHYDPLQRNFP
                     DPDTPPLTIFSSNDDIVLVQALELADEARRRRQFTDVNRFTLRCMVCQKGLTGQAEAR
                     EHAKETGHTNFGEV"
     exon            522..6396
                     /gene="YOD1"
                     /gene_synonym="DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907"
                     /inference="alignment:Splign:2.1.0"
     regulatory      6377..6382
                     /regulatory_class="polyA_signal_sequence"
                     /gene="YOD1"
                     /gene_synonym="DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907"
                     /note="hexamer: AATAAA"
     polyA_site      6396
                     /gene="YOD1"
                     /gene_synonym="DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907"
                     /note="major polyA site"
ORIGIN      
        1 actcgctcta taggtagcaa gacccgttgt cctttaggaa tacggaggtt tacatcttcg
       61 ttctgagggt gggggaaaaa tcagttgtca ctttaaaaga gttcgcgctt gctaaggtac
      121 taaggcagaa gccgcaccga agcgtcgcga taactgcaac cacccgcaac ttctcgcgat
      181 gtttggcccc gctaaaggtc gccattttgg agtccacccg gcgcctggtt tccccggcgg
      241 cgtctcccaa caggctgccg ggaccaaagc tggccccgcg ggtgcctggc ctgtgggcag
      301 ccggaccgac acgatgtggc ggctccgctg caaggccaag gacggcaccc atgttttgca
      361 ggggctgtcc agccggaccc gggtgcggga actccagggc caaattgccg ccatcaccgg
      421 gatcgccccc ggcggtcagc gaatcctcgt cggataccct cccgagtgcc tggatctcag
      481 caatggggat accattctgg aagacttgcc catccaatct ggtgacatgc tgatcattga
      541 agaagaccaa accaggccca gaagttcacc tgcatttact aaacgtggtg cttctagtta
      601 cgtcagggaa actttgcctg tgcttaccag aaccgtggtc ccagcagaca actcttgcct
      661 ctttactagt gtgtactatg tcgtcgaagg aggagtcttg aatccagctt gtgcccctga
      721 gatgagacgc ctcatagcac aaattgtagc aagcgatcca gacttctata gtgaggcaat
      781 actgggaaaa acaaatcaag agtactgtga ctggatcaaa agggatgaca cttggggagg
      841 agcaatagag atatcgattt tgtccaagtt ttaccaatgt gaaatatgtg tagtggatac
      901 acagacagta agaattgatc gttttgggga agatgcagga tataccaaaa gggttctgct
      961 tatttatgat ggcatccact atgatccact tcagcgtaac ttccctgatc cagatacacc
     1021 tcctctgacc attttctcct ctaatgatga tattgttctt gtacaagcac tggaattagc
     1081 agatgaagct agaagaagga gacagtttac tgatgtcaac cgcttcaccc tgagatgcat
     1141 ggtatgtcag aaaggattaa ctggacaagc agaagcaagg gaacatgcca aggagacagg
     1201 ccataccaac tttggagaag tgtgacctat gcatgaatga gggttgaagc ctactacctc
     1261 acacatccag aaggctctgg gttttccaat aagctatggt aaccctaaag aacaaaggat
     1321 acaatgcttg aaccatcctt ttaacttaaa accactaaga cactgaaatt ccttgttaag
     1381 attaaaatta gtgtgcaagt ttacagatgt gtgtctacag tggtaaactg tacatacatg
     1441 cctctttctg ctggagtgac agaataggtg atccttgcca cctactgaca ctgacctgaa
     1501 ggttgagatt gagtattata aactagcacc cagcagcttt aacttgtaga agaaagcatc
     1561 acattttggg taatgtggaa ggcctcctgt gagtccactg ggcatacgat tgagattgag
     1621 tattataaac tagcacccag cagctttaac ttgtagaaga aagcatcaca ttttgggtaa
     1681 tgtggaaggc ctcctgtgag tccactggac atttaccaca gtgtctccag taactgagtc
     1741 tttttaaaaa ctctgaatga gttaagtttc taaattatga attgattcat caaatgaaga
     1801 tactcagaat tgtccaaact gattttatat tgcaatttgg tagacattat aaatgtgtgc
     1861 ttaaccactg ataagtacat cacaagcaat ttttacaggg atgagtctca tccttgagaa
     1921 tgttatcaca aaacaggaac tgattgtgcc ctgtttaaga tctctagcat ataaaacgta
     1981 gaatgtatga gggaataggt gcctgagcag cttcctgaag ctttaaaaga ccgttggcct
     2041 cgtgttttaa tgcaattcat gtattggtct ttgtcacatt ggataacatt ttaaagttaa
     2101 gcagggtact tttttaattg aaattccttg aaattcgagt cctcagtttt ttcttcattt
     2161 gcgtaaagtt tatcgggggg aatttaattt tctcagcttt ttgttaagag cacttcctcc
     2221 aaaaaatttt tttcaagtaa taatgctctg ctttgggttg gtttttgtaa gattttttgc
     2281 acacctaaag agtgtttgct tttgtgctag ccttatccct ccactaaagt tattttaaat
     2341 aatttcacat ttctgcaaat tagcactttg cttatctgca atcttttact ttgatttttg
     2401 aagttttaaa gcaattggag taatactgtt gaatgaacta gtttcacttc caaaatagaa
     2461 aaaattgtaa atccttgcct tatgcagctt tctcagaatt ctgcttcttc ctagtactag
     2521 atgtgtagcc atttgcttag tggactaatc cgcaaggcac accctctaaa acttagcttc
     2581 actacaagat cttccagata aaagttttct acctcttttc ttaattattc tgatcaggga
     2641 tgctaaatta taatttgtta tgtattatct cacataatgt gaagaggctt aatgtgaagt
     2701 tttgttattt tggtctcttt tttattaagt atctcactta gaaattcagt ggtatacttt
     2761 aaagcacttg gatctttttc agcatatctg cctagcaaat gttttaaaat tgacatttat
     2821 ttttagcact ttcacttggt gaaggtggcc atataaaatt aaggaacatt tgaacaatat
     2881 aagagaaaag aacttttaag gaacaattca caaagtttgt ttgaaattgt cagatgacat
     2941 ttcttgagta ccttttgtgt gcatagttat tttagacaat ataagctgtt atggtcagca
     3001 taacttaaaa gtgtttagtt ttctatttta ctgagcctta aaaatagcac tgatgagctt
     3061 atgatactta atgtttggca atcataatgt gttcaaatta atgggattga aaatctctcc
     3121 acacctgact ctcatctgat ctggatggtt ttggttttgt atctttttta cttctcccag
     3181 aaaatactaa atttaaaact gtaaattaag aatataccac tagataacaa ttatcaaatt
     3241 gagctttatg catcattact cagaaagctt gccttccttt ctttgctact tcaggacaca
     3301 gagttgacat ttgcttacta cagctttaga tctagaagtt tattcgtgca acaaatattt
     3361 attgagtaat ttatactgtg ccaggcatgt tttgatatgt ttctgtcata tgttttgata
     3421 tgttccaaca taagtttctg tcactttata ttcagtatat attttctaca gtgggtaaat
     3481 ttaacaaatg gaaaggaata gaacactgat attttacaga attaaacccc ttcattgtaa
     3541 gggctttgtt tacatattaa gtgtcaagta tttattcagg ggatcttatt tcattgtatt
     3601 ttatctgtta tctaggttgt ccatttaccg gttggacact gatactctgt caaattcctt
     3661 tcaaaaatga ctctttagtc tgctgaaatt tagcactagt actttagtgt tctgatcctg
     3721 gaaaattcaa ggtgaagctt tatttgtgga ccatctgatt taattattga ggattaaaaa
     3781 cctaaacctt tgctcattct aaactcaagc ttttaagcct cacagaattt acaggggttt
     3841 gctttttgtt tgtttgtttt ttcatttttt actgtgctta ttaaactctt ggaattagtt
     3901 attaaaggga gtaaattctc atcttgggaa ttttgaaaat ctatggactt acaactttca
     3961 ggaggattaa atgtcttaag ttttgtacta gagcagaatg aaatctttcc tattcattga
     4021 gtttttgcct gccatagagg aattttttta aaaattaaaa tgacagttta tattagtggc
     4081 aaagtgaata aagacctcac tttcccaccc cacccttctt cctttctctt acttttcttt
     4141 ggattaaagg tcaggtgtag tactatgaag attcactcct gaataaagtg atttcagaag
     4201 ctaaaattta acatacctgg aaattttgtg atgtgttagc caagtgaaga cattagtgtg
     4261 ttccatcttt tgctaatggt tcatggttga tttcttcatt gtttcccatg aaattagcat
     4321 agtcaagtgg tacccttgac gcttgactgc tggtcagttt gaccctgttt ttaacaacta
     4381 atgtagtcat gccgcttgat tattccatga agtcccagca aaataataat gaggaattaa
     4441 ctaacattat gttatctatc taatttgtct gtgtccctaa atgcccatgc ctaacttgct
     4501 tctctagttt attccttctg tggagggatt aaaacgtggg tgttgcaagt tgccctaagc
     4561 taaacatagt tttcttacat ctttttggga aaaaaaatgg aatgggaagt atgcaagatt
     4621 aagcaagagt gatttttttt tttttttgac aaatcaggtg gccttcctaa acatactaag
     4681 aattatgttc tttcatgtgt ggagacacat ttgtttgcag cactttaaaa aatatatatg
     4741 gaataaaagt ttacatgttg gccctctagg gatctaatta aggacattaa agtacaattc
     4801 ttgagctact aaccatcagc tcttcttaat caaagattgc catcagtgta gagtgtatct
     4861 attggcacaa cattctggtg ttttgataac agtagaactc aatttcagta actattagga
     4921 gcatggtctg tgccctagca ttaaaaatgt tacttattat tatgtgaata tcttgtatta
     4981 ttatacaatg cagtattcaa atttgtcctt gtagtgcaga gatgactgat aatttctaaa
     5041 agattcgatc cttaaaactt gtttccaagc agacttataa ggaagctgat ttttgagtca
     5101 gaggccttaa acgtgtcata tacaagtggc atcattttaa gtccaaagtg aaacacttga
     5161 tttgaataag ctagtttata aactaaagct gttttcttat gttacagtat ttcagcacat
     5221 ttcattccac ataaaaagaa tattaagtgt ccctggttgt gggagagtgt ttatttttct
     5281 caaaattatc tagcattttg cttacagtgc tttgaatgtt tgacttaaaa ttattattga
     5341 tgttgaattg tagggtgctg atttaggtct tgattcatac acatttaaag gaggttggta
     5401 accccctcat ggtagagtga agggagaaaa gggccaagaa gacaaagtac cactgataaa
     5461 gaagagattg tcaaatagat gcattcctag tcatgaatta cccttttcca aacattttta
     5521 aagcaatgcc tttgtgtcaa ctcaaccctt cttccccatt tcttgtcata gaatgtagca
     5581 tggccatagg tgaaaaagct tatcattaaa gtatgaaacc atgaattata agcattttgc
     5641 catgatgccc ttttatacat atgtttttaa aagtactaac caacatatag gagtttagga
     5701 atggtgaaga tataatttga ttaagttgta ggtaaacaga aaggatcatc ttaggctcag
     5761 aatttctaat atgattacat gagtctactt tataaactgg tataggctat gtaattagcc
     5821 cgtaagttac ttaaaggacc aggggaccta atttttgtca gttttccagt cacattggtg
     5881 ccattcagga ctccagctgt ttacaggaaa tatgtactta gcagaatagt atttttcctt
     5941 gaaaaaaatt tgaattcagc ctaaatacag aatgaatatg aatagtttgt gaaaagggtt
     6001 agagaacaac aatattccta tagtttctgt attaatgcag tagagacaga ggttcctaac
     6061 gcaaaaagaa aaccacaagt aaagaccgtc aaattagagc tttagaatat gacttgaaaa
     6121 agtagggatg ggcaaaacag cataagaaaa tattttttct taatgcagat ggacagtgtt
     6181 ttcttgtttt aaaaatgttt tgcctatttg ccagcatttt ttgaagtaat acactgctgc
     6241 tacctggaag atgtctaact tcattttcta caactcttat gtgattttgc cattgtcatt
     6301 aagatgcatt gattttattt atgaggtgta tgactttaaa tatctaaatg ctgtattaag
     6361 tgacttgttt caaaggaata aatgaagtga aaacgt
//
