LOCUS       NM_001376665            2542 bp    mRNA    linear   PRI 12-FEB-2025
DEFINITION  Homo sapiens MINDY lysine 48 deubiquitinase 1 (MINDY1), transcript
            variant 8, mRNA.
ACCESSION   NM_001376665 XM_017001772
VERSION     NM_001376665.1
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 2542)
  AUTHORS   Abdul Rehman,S.A., Armstrong,L.A., Lange,S.M., Kristariyanto,Y.A.,
            Grawert,T.W., Knebel,A., Svergun,D.I. and Kulathu,Y.
  TITLE     Mechanism of activation and regulation of deubiquitinase activity
            in MINDY1 and MINDY2
  JOURNAL   Mol Cell 81 (20), 4176-4190 (2021)
   PUBMED   34529927
  REMARK    GeneRIF: Mechanism of activation and regulation of deubiquitinase
            activity in MINDY1 and MINDY2.
REFERENCE   2  (bases 1 to 2542)
  AUTHORS   Tang,J., Luo,Y., Long,G. and Zhou,L.
  TITLE     MINDY1 promotes breast cancer cell proliferation by stabilizing
            estrogen receptor alpha
  JOURNAL   Cell Death Dis 12 (10), 937 (2021)
   PUBMED   34645792
  REMARK    GeneRIF: MINDY1 promotes breast cancer cell proliferation by
            stabilizing estrogen receptor alpha.
            Erratum:[Cell Death Dis. 2022 Jan 27;13(1):88. doi:
            10.1038/s41419-022-04549-7.. PMID: 35087032]
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2542)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   4  (bases 1 to 2542)
  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   5  (bases 1 to 2542)
  AUTHORS   Kristariyanto,Y.A., Abdul Rehman,S.A., Weidlich,S., Knebel,A. and
            Kulathu,Y.
  TITLE     A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin
            chains
  JOURNAL   EMBO Rep 18 (3), 392-402 (2017)
   PUBMED   28082312
REFERENCE   6  (bases 1 to 2542)
  AUTHORS   Abdul Rehman,S.A., Kristariyanto,Y.A., Choi,S.Y., Nkosi,P.J.,
            Weidlich,S., Labib,K., Hofmann,K. and Kulathu,Y.
  TITLE     MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally
            Distinct New Family of Deubiquitinating Enzymes
  JOURNAL   Mol Cell 63 (1), 146-155 (2016)
   PUBMED   27292798
  REMARK    GeneRIF: MINDY-1 prefers cleaving long polyubiquitin chains and
            works by trimming chains from the distal end.
REFERENCE   7  (bases 1 to 2542)
  AUTHORS   Kirin,M., Chandra,A., Charteris,D.G., Hayward,C., Campbell,S.,
            Celap,I., Bencic,G., Vatavuk,Z., Kirac,I., Richards,A.J.,
            Tenesa,A., Snead,M.P., Fleck,B.W., Singh,J., Harsum,S.,
            Maclaren,R.E., den Hollander,A.I., Dunlop,M.G., Hoyng,C.B.,
            Wright,A.F., Campbell,H., Vitart,V. and Mitry,D.
  TITLE     Genome-wide association study identifies genetic risk underlying
            primary rhegmatogenous retinal detachment
  JOURNAL   Hum Mol Genet 22 (15), 3174-3185 (2013)
   PUBMED   23585552
REFERENCE   8  (bases 1 to 2542)
  AUTHORS   Kottgen,A., Pattaro,C., Boger,C.A., Fuchsberger,C., Olden,M.,
            Glazer,N.L., Parsa,A., Gao,X., Yang,Q., Smith,A.V., O'Connell,J.R.,
            Li,M., Schmidt,H., Tanaka,T., Isaacs,A., Ketkar,S., Hwang,S.J.,
            Johnson,A.D., Dehghan,A., Teumer,A., Pare,G., Atkinson,E.J.,
            Zeller,T., Lohman,K., Cornelis,M.C., Probst-Hensch,N.M.,
            Kronenberg,F., Tonjes,A., Hayward,C., Aspelund,T., Eiriksdottir,G.,
            Launer,L.J., Harris,T.B., Rampersaud,E., Mitchell,B.D.,
            Arking,D.E., Boerwinkle,E., Struchalin,M., Cavalieri,M.,
            Singleton,A., Giallauria,F., Metter,J., de Boer,I.H.,
            Haritunians,T., Lumley,T., Siscovick,D., Psaty,B.M.,
            Zillikens,M.C., Oostra,B.A., Feitosa,M., Province,M., de
            Andrade,M., Turner,S.T., Schillert,A., Ziegler,A., Wild,P.S.,
            Schnabel,R.B., Wilde,S., Munzel,T.F., Leak,T.S., Illig,T.,
            Klopp,N., Meisinger,C., Wichmann,H.E., Koenig,W., Zgaga,L.,
            Zemunik,T., Kolcic,I., Minelli,C., Hu,F.B., Johansson,A., Igl,W.,
            Zaboli,G., Wild,S.H., Wright,A.F., Campbell,H., Ellinghaus,D.,
            Schreiber,S., Aulchenko,Y.S., Felix,J.F., Rivadeneira,F.,
            Uitterlinden,A.G., Hofman,A., Imboden,M., Nitsch,D.,
            Brandstatter,A., Kollerits,B., Kedenko,L., Magi,R., Stumvoll,M.,
            Kovacs,P., Boban,M., Campbell,S., Endlich,K., Volzke,H.,
            Kroemer,H.K., Nauck,M., Volker,U., Polasek,O., Vitart,V.,
            Badola,S., Parker,A.N., Ridker,P.M., Kardia,S.L., Blankenberg,S.,
            Liu,Y., Curhan,G.C., Franke,A., Rochat,T., Paulweber,B.,
            Prokopenko,I., Wang,W., Gudnason,V., Shuldiner,A.R., Coresh,J.,
            Schmidt,R., Ferrucci,L., Shlipak,M.G., van Duijn,C.M., Borecki,I.,
            Kramer,B.K., Rudan,I., Gyllensten,U., Wilson,J.F., Witteman,J.C.,
            Pramstaller,P.P., Rettig,R., Hastie,N., Chasman,D.I., Kao,W.H.,
            Heid,I.M. and Fox,C.S.
  TITLE     New loci associated with kidney function and chronic kidney disease
  JOURNAL   Nat Genet 42 (5), 376-384 (2010)
   PUBMED   20383146
REFERENCE   9  (bases 1 to 2542)
  AUTHORS   Lehner,B. and Sanderson,C.M.
  TITLE     A protein interaction framework for human mRNA degradation
  JOURNAL   Genome Res 14 (7), 1315-1323 (2004)
   PUBMED   15231747
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL590133.32.
            
            On Nov 18, 2019 this sequence version replaced XM_017001772.2.
            
            Transcript Variant: This variant (8) differs in the 5' UTR,
            compared to variant 1. Variants 1, 3, 6 and 8 encode the same
            isoform (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1803617.113832.1,
                                           SRR1803615.193913.1 [ECO:0000332]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000683666.2/ ENSP00000507359.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-591               AL590133.32        92505-93095         c
            592-1133            AL590133.32        88358-88899         c
            1134-1191           AL590133.32        87918-87975         c
            1192-1256           AL590133.32        87443-87507         c
            1257-1415           AL590133.32        86650-86808         c
            1416-1518           AL590133.32        86055-86157         c
            1519-1661           AL590133.32        85562-85704         c
            1662-1853           AL590133.32        84275-84466         c
            1854-2009           AL590133.32        83817-83972         c
            2010-2542           AL590133.32        83028-83560         c
FEATURES             Location/Qualifiers
     source          1..2542
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q21.3"
     gene            1..2542
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /note="MINDY lysine 48 deubiquitinase 1"
                     /db_xref="GeneID:55793"
                     /db_xref="HGNC:HGNC:25648"
                     /db_xref="MIM:618407"
     exon            1..591
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     exon            592..1133
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     CDS             681..2090
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /EC_number="3.4.19.12"
                     /note="isoform 1 is encoded by transcript variant 8;
                     protein FAM63A; deubiquitinating enzyme MINDY-1; ubiquitin
                     carboxyl-terminal hydrolase MINDY-1; MIU-containing novel
                     DUB family member 1; motif interacting with Ub-containing
                     novel DUB; family with sequence similarity 63 member A;
                     MINDY deubiquitinase 1"
                     /codon_start=1
                     /product="ubiquitin carboxyl-terminal hydrolase MINDY-1
                     isoform 1"
                     /protein_id="NP_001363594.1"
                     /db_xref="CCDS:CCDS976.1"
                     /db_xref="GeneID:55793"
                     /db_xref="HGNC:HGNC:25648"
                     /db_xref="MIM:618407"
                     /translation="MEYHQPEDPAPGKAGTAEAVIPENHEVLAGPDEHPQDTDARDAD
                     GEAREREPADQALLPSQCGDNLESPLPEASSAPPGPTLGTLPEVETIRACSMPQELPQ
                     SPRTRQPEPDFYCVKWIPWKGEQTPIITQSTNGPCPLLAIMNILFLQWKVKLPPQKEV
                     ITSDELMAHLGNCLLSIKPQEKSEGLQLNFQQNVDDAMTVLPKLATGLDVNVRFTGVS
                     DFEYTPECSVFDLLGIPLYHGWLVDPQSPEAVRAVGKLSYNQLVERIITCKHSSDTNL
                     VTEGLIAEQFLETTAAQLTYHGLCELTAAAKEGELSVFFRNNHFSTMTKHKSHLYLLV
                     TDQGFLQEEQVVWESLHNVDGDSCFCDSDFHLSHSLGKGPGAEGGSGSPETQLQVDQD
                     YLIALSLQQQQPRGPLGLTDLELAQQLQQEEYQQQQAAQPVRMRTRVLSLQGRGATSG
                     RPAGERRQRPKHESDCILL"
     exon            1134..1191
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1192..1256
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1257..1415
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1416..1518
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1519..1661
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1662..1853
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     exon            1854..2009
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     exon            2010..2542
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2522..2527
                     /regulatory_class="polyA_signal_sequence"
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /note="hexamer: AATAAA"
     polyA_site      2542
                     /gene="MINDY1"
                     /gene_synonym="FAM63A; MINDY-1"
                     /note="major polyA site"
ORIGIN      
        1 agagaggcac aagcgctccg tcccttctag aggcaggcag agggaagaga aagggtctgt
       61 tgtttttctc tcctgtttct cgctccctct ctgctgatca caaagctgct gaccgggtca
      121 gaaagtcctg atggaaatcc accagcgctg ggcaggcccc tcctcctcca gggagcttgt
      181 ccttgcctaa tttttcttcg tcctgatgag aacaaaaaag agagagagaa gaaaagaaaa
      241 accacaaact tcctttgaaa accagcttgt agtcagggcc cggagcgcat gccatagact
      301 cggcgactca ggaatcctga agactctctg agcgacctgg agcaccttgg ctgtgtccct
      361 gcctgccttc accctcctcc agtgccccca gtactgggcg tgagtccgga agtggccaca
      421 acccagcctg gaccgtcgct tataaagctg tgtaaacctg tataagctca ggcgttgaca
      481 gctggaaggc agctggcact ggcagccccc ttcattgcac ctatctcccc catctcattg
      541 ccacggctga accctccttc tcaatcttgg aacagcaccc ccttctttaa ggtcactctt
      601 ttgcatccca agcctggctt aggcaagtcc ctgaggttag taaacacctt cagtgcccct
      661 cagccaagtc ccttttgacc atggaatacc atcagcctga ggatccagcc cctggtaagg
      721 ccgggactgc agaagcagtc atccctgaaa accatgaggt tctggcaggc ccagatgagc
      781 accctcagga cacagatgca agagatgctg atggggaggc tagagaacgg gagccagcag
      841 accaagcttt gctgcctagc cagtgtgggg acaaccttga gtcccctctg cctgaagcta
      901 gctcagctcc accggggcca acccttggga cactgcctga agtagagaca ataagggcat
      961 gctccatgcc ccaggagctt cctcagtccc ccaggacccg acagcctgag ccagatttct
     1021 actgtgtcaa gtggatccct tggaaaggag aacagacacc catcatcacc cagagcacta
     1081 acggcccttg ccctctcctt gccatcatga acatcctctt tcttcagtgg aaggtgaagc
     1141 tccccccgca gaaggaagtg atcacatcgg atgagctcat ggcccatctt ggaaactgcc
     1201 tcctgtccat caagccccag gagaagtcag agggacttca gcttaatttt cagcagaatg
     1261 tggatgatgc aatgacagtg ctgcctaaac tggccacagg tctggatgtc aatgtgcgat
     1321 tcacaggcgt ctctgatttt gagtatacac ccgagtgcag tgtctttgac ctgctaggca
     1381 tacctctgta ccatggctgg cttgttgatc cacagagtcc tgaggctgtg cgtgcagttg
     1441 ggaaactgag ttacaaccag ctggtggaga ggatcatcac ctgcaaacac tccagtgaca
     1501 ccaacctcgt gacagaaggc ctgattgcag agcagttcct ggagaccacc gcggcccagc
     1561 tgacctacca cggactgtgt gagctgacag cagctgctaa ggagggtgaa cttagcgtct
     1621 ttttccgaaa caaccacttt agcaccatga ctaagcataa gagtcactta tacctactgg
     1681 tcactgacca gggctttcta caggaggagc aagtcgtatg ggagagcctg cacaatgtgg
     1741 atggagacag ctgcttttgt gactctgact ttcacctgag tcattccctg ggcaaggggc
     1801 ctggagcaga aggtgggagt ggctccccag aaacgcagct gcaggtagac caggactacc
     1861 tgattgctct gtccctgcag cagcaacagc cacgaggccc gctggggctt accgacttgg
     1921 agctggccca gcagcttcag caagaggagt atcaacagca gcaggcagcg cagccagtgc
     1981 ggatgcggac gcgggtcctg tcactgcagg ggagaggagc cacatctgga cgcccagccg
     2041 gggagcgtcg gcagaggccg aagcacgagt cagactgcat tctgctgtag ctctgcccca
     2101 gtgccaggct ggcctgcccc ttcttccaga ggctatggct agttggcttg ctcccccgcc
     2161 tccacccctg agatgtgctg gataacttat ttatggactg ttggggatga gagcaggcaa
     2221 caaatgccaa ggtcagactt ggtaatgtcc ttgacctcac gtgctgctgc cttctctgcc
     2281 tcccatccag ggcaacacta ggattggtgg gtttctggtt ctcaactccc ggtccctgaa
     2341 tagtcacacg tatgtacaga ctgaggctct ggggtgaggt ccctatccag aatgcatctc
     2401 ttctgcttcc catccctgct gcctggatgc tcctgatcac ctaggcaggc ctgtctccag
     2461 ttgtttcaga gcttaatttg ggtttctatc tcttatttgt aatgccttcc tggggtttgg
     2521 aaataaaact tctggccggg ca
//
