LOCUS       NM_145062               2167 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens zinc finger containing ubiquitin peptidase 1 (ZUP1),
            transcript variant 1, mRNA.
ACCESSION   NM_145062
VERSION     NM_145062.3
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 2167)
  AUTHORS   Ajadi,M.B., Soremekun,O.S., Adewumi,A.T., Kumalo,H.M. and
            Soliman,M.E.S.
  TITLE     Functional Analysis of Single Nucleotide Polymorphism in ZUFSP
            Protein and Implication in Pathogenesis
  JOURNAL   Protein J 40 (1), 28-40 (2021)
   PUBMED   33512633
  REMARK    GeneRIF: Functional Analysis of Single Nucleotide Polymorphism in
            ZUFSP Protein and Implication in Pathogenesis.
REFERENCE   2  (bases 1 to 2167)
  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   3  (bases 1 to 2167)
  AUTHORS   Haahr,P., Borgermann,N., Guo,X., Typas,D., Achuthankutty,D.,
            Hoffmann,S., Shearer,R., Sixma,T.K. and Mailand,N.
  TITLE     ZUFSP Deubiquitylates K63-Linked Polyubiquitin Chains to Promote
            Genome Stability
  JOURNAL   Mol Cell 70 (1), 165-174 (2018)
   PUBMED   29576528
  REMARK    GeneRIF: ZUFSP is recruited to and regulates K63-Ub conjugates at
            genotoxic stress sites, promoting chromosome stability upon
            replication stress in a manner dependent on its catalytic activity.
REFERENCE   4  (bases 1 to 2167)
  AUTHORS   Kwasna,D., Abdul Rehman,S.A., Natarajan,J., Matthews,S., Madden,R.,
            De Cesare,V., Weidlich,S., Virdee,S., Ahel,I., Gibbs-Seymour,I. and
            Kulathu,Y.
  TITLE     Discovery and Characterization of ZUFSP/ZUP1, a Distinct
            Deubiquitinase Class Important for Genome Stability
  JOURNAL   Mol Cell 70 (1), 150-164 (2018)
   PUBMED   29576527
  REMARK    GeneRIF: Identify two ubiquitin binding domains in ZUFSP: a ZHA
            (ZUFSP helical arm) that binds to the distal ubiquitin and an
            atypical UBZ domain in ZUFSP that binds to polyubiquitin.
            Importantly, both domains are essential for ZUFSP to selectively
            cleave K63-linked polyubiquitin.
REFERENCE   5  (bases 1 to 2167)
  AUTHORS   Hermanns,T., Pichlo,C., Woiwode,I., Klopffleisch,K., Witting,K.F.,
            Ovaa,H., Baumann,U. and Hofmann,K.
  TITLE     A family of unconventional deubiquitinases with modular chain
            specificity determinants
  JOURNAL   Nat Commun 9 (1), 799 (2018)
   PUBMED   29476094
  REMARK    GeneRIF: ZUFSP,the singular human member of this family, which
            contains multiple ubiquitin-binding domains responsible for the
            specific action on K63-linked chains.
            GeneRIF: ZUFSP (ZUP1) is a K63-specific deubiquitinating enzyme
            that is distantly related to proteases for the ubiquitin-like
            modifiers Ufm1 and Atg8. ZUFSP does not have any activity on these
            modifiers. ZUFSP specifically cleaves long K63-linked
            poly-ubiquitin chains in an ''endo'' mode, i.e. cleavage takes
            place in the middle of a chain rather than by removing the terminal
            ubiquitin from a chain.
            Publication Status: Online-Only
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC016879.1.
            
            On Nov 22, 2018 this sequence version replaced NM_145062.2.
            
            Summary: This gene encodes a protein containing zinc finger motifs
            and a cysteine peptidase domain. The encoded protein functions as a
            K63-specific de-ubiquitinating enzyme that specifically cleaves
            long K63-linked polyubiquitin chains in the middle of a chain (i.e.
            'endo cleavage) rather than by removing the terminal ubiquitin from
            a chain. This enzyme is thought to be involved in the regulation of
            DNA repair by cleaving K63-linked ubiquitin chains at repair foci.
            This protein is related to proteases for the ubiquitin-like
            modifiers Ufm1 (ubiquitin fold modifier 1) and Atg8/Gabarapl2, but
            does not have any activity on these modifiers. [provided by RefSeq,
            Mar 2018].
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC016879.1, AK054582.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000368576.8/ ENSP00000357565.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2167              BC016879.1         13-2179
FEATURES             Location/Qualifiers
     source          1..2167
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6q22.1"
     gene            1..2167
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /note="zinc finger containing ubiquitin peptidase 1"
                     /db_xref="GeneID:221302"
                     /db_xref="HGNC:HGNC:21224"
                     /db_xref="MIM:620543"
     exon            1..201
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     exon            202..775
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     CDS             217..1953
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /EC_number="3.4.19.12"
                     /note="isoform 1 is encoded by transcript variant 1; zinc
                     finger with UFM1-specific peptidase domain protein;
                     lys-63-specific deubiquitinase ZUFSP; ubiquitin
                     carboxyl-terminal hydrolase ZUFSP"
                     /codon_start=1
                     /product="zinc finger-containing ubiquitin peptidase 1
                     isoform 1"
                     /protein_id="NP_659499.2"
                     /db_xref="CCDS:CCDS5110.1"
                     /db_xref="GeneID:221302"
                     /db_xref="HGNC:HGNC:21224"
                     /db_xref="MIM:620543"
                     /translation="MLSCNICGETVTSEPDMKAHLIVHMESEIICPFCKLSGVNYDEM
                     CFHIETAHFEQNTLERNFERINTVQYGTSDNKKDNTLQCGMEVNSSILSGCASNHPKN
                     SAQNLTKDSTLKHEGFYSENLTESRKFLKSREKQSSLTEIKGSVYETTYSPPECPFCG
                     KIEEHSEDMETHVKTKHANLLDIPLEDCDQPLYDCPMCGLICTNYHILQEHVDLHLEE
                     NSFQQGMDRVQCSGDLQLAHQLQQEEDRKRRSEESRQEIEEFQKLQRQYGLDNSGGYK
                     QQQLRNMEIEVNRGRMPPSEFHRRKADMMESLALGFDDGKTKTSGIIEALHRYYQNAA
                     TDVRRVWLSSVVDHFHSSLGDKGWGCGYRNFQMLLSSLLQNDAYNDCLKGMLIPCIPK
                     IQSMIEDAWKEGFDPQGASQLNNRLQGTKAWIGACEVYILLTSLRVKCHIVDFHKSTG
                     PLGTHPRLFEWILNYYSSEGEGSPKVVCTSKPPIYLQHQGHSRTVIGIEEKKNRTLCL
                     LILDPGCPSREMQKLLKQDIEASSLKQLRKSMGNLKHKQYQILAVEGALSLEEKLARR
                     QASQVFTAEKIP"
     exon            776..886
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     exon            887..1008
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     exon            1009..1177
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     exon            1178..1366
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     exon            1367..1532
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     exon            1533..1684
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     exon            1685..1905
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     exon            1906..2167
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2141..2146
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /note="hexamer: AATAAA"
     polyA_site      2167
                     /gene="ZUP1"
                     /gene_synonym="C6orf113; DUB; ZUFSP"
                     /note="major polyA site"
ORIGIN      
        1 gaatgaggta ctgagggcca aggtgttgga agttcctaat tctttcctcg gttaactgtg
       61 aaactctgcg tattgggaag gcctggcctc agtcatcagg ccaggagagg tactggacgc
      121 cgcgcacgca ctcgtctgcc agcgaggccc aaaggggaag cctagcggag ctcagtgtgg
      181 cagctgctgg cctctgggcc gctacttgtc aataccatgc tttcctgtaa tatttgtggt
      241 gaaacagtaa cctcagaacc agacatgaaa gctcacctaa ttgttcacat ggaaagtgaa
      301 attatatgtc cattttgcaa gttgtcaggt gtgaattatg atgaaatgtg ttttcatatc
      361 gaaacagctc attttgagca gaatacactt gaaagaaact ttgagaggat aaatacagta
      421 caatatggaa cttcagataa caagaaagac aacaccctac agtgtggaat ggaagttaat
      481 tcaagtattc tttcaggttg tgcatctaat catccaaaaa attcagctca aaacctgact
      541 aaagatagta ctttaaaaca tgaaggcttc tattcagaga acttaactga atctagaaaa
      601 ttcctgaaaa gtagggaaaa acagtccagc ctgaccgaaa taaaaggatc tgtttatgaa
      661 acaacataca gtcctcctga atgtccattc tgtggaaaaa tagaggagca cagtgaagat
      721 atggaaactc atgtgaaaac aaagcatgcc aatcttttag acattccatt ggaagactgt
      781 gatcaaccac tctatgattg tcctatgtgt gggctcatat gtacaaatta ccatattctt
      841 caggaacatg ttgacttgca tttggaagaa aacagctttc agcaaggcat ggatagagtc
      901 cagtgttctg gtgatctaca attggctcac cagcttcagc aagaagaaga cagaaagagg
      961 agatctgaag aatcaagaca agaaatagaa gaatttcaga agctgcagag acaatatggt
     1021 ttagataatt ctggaggata caaacaacaa caactacgaa atatggagat agaagtaaat
     1081 aggggaagaa tgcctccatc tgaatttcat aggagaaaag ctgatatgat ggaatcatta
     1141 gctcttggtt ttgacgatgg aaaaacaaaa acttccggaa ttattgaagc acttcatagg
     1201 tattatcaga atgctgccac agatgtgaga cgggtgtggc tttcttcagt ggtggatcac
     1261 tttcattcat ctttaggcga caaaggttgg ggttgtggtt acagaaattt ccaaatgcta
     1321 ctttcatcat tattacaaaa tgatgcttac aacgattgct taaaaggtat gttgattcct
     1381 tgcattccaa aaattcaatc tatgattgaa gatgcatgga aggaaggttt tgatcctcag
     1441 ggggcctctc aacttaataa caggttacag ggaacaaagg cctggattgg agcatgtgaa
     1501 gtatatatac tcctgacctc cctaagggta aagtgtcata ttgttgattt tcacaaatca
     1561 actggtcctt tgggtacaca ccctcgctta tttgaatgga tattgaacta ttattcttca
     1621 gagggagaag ggagtccaaa ggtagtgtgt acatctaaac ctcctatcta tcttcagcat
     1681 caaggtcaca gtcgaactgt tattggaatt gaagagaaaa aaaaccgaac attatgctta
     1741 ctaatacttg atcctggatg tccttctcga gaaatgcaga aattattaaa gcaagacata
     1801 gaggctagca gtctcaagca acttcggaaa tctatgggaa atttaaaaca taagcaatac
     1861 cagatattgg cagtagaggg tgctctttct ctagaggaga aacttgccag gagacaagct
     1921 tctcaagtct ttacagccga gaagattcct tgaagaatca agcatttaag catttcagtg
     1981 attgagaaca atactttgtt ttctaaatgt agatattgaa ctccttaata caattatgaa
     2041 tctgtgaatt ctcttaagtc ttaacatata atttaatttc taaaatgcct gtgttaattg
     2101 aattatacct atcatacttc attgtttggt aaattatttc aataaaatgt cttgtttttg
     2161 cattgtg
//
