LOCUS       NM_152616               2514 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens tripartite motif containing 42 (TRIM42), mRNA.
ACCESSION   NM_152616
VERSION     NM_152616.5
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 2514)
  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   2  (bases 1 to 2514)
  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 2514)
  AUTHORS   Fragoza,R., Das,J., Wierbowski,S.D., Liang,J., Tran,T.N., Liang,S.,
            Beltran,J.F., Rivera-Erick,C.A., Ye,K., Wang,T.Y., Yao,L., Mort,M.,
            Stenson,P.D., Cooper,D.N., Wei,X., Keinan,A., Schimenti,J.C.,
            Clark,A.G. and Yu,H.
  TITLE     Extensive disruption of protein interactions by genetic variants
            across the allele frequency spectrum in human populations
  JOURNAL   Nat Commun 10 (1), 4141 (2019)
   PUBMED   31515488
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2514)
  AUTHORS   Yang,X., Coulombe-Huntington,J., Kang,S., Sheynkman,G.M., Hao,T.,
            Richardson,A., Sun,S., Yang,F., Shen,Y.A., Murray,R.R., Spirohn,K.,
            Begg,B.E., Duran-Frigola,M., MacWilliams,A., Pevzner,S.J.,
            Zhong,Q., Wanamaker,S.A., Tam,S., Ghamsari,L., Sahni,N., Yi,S.,
            Rodriguez,M.D., Balcha,D., Tan,G., Costanzo,M., Andrews,B.,
            Boone,C., Zhou,X.J., Salehi-Ashtiani,K., Charloteaux,B., Chen,A.A.,
            Calderwood,M.A., Aloy,P., Roth,F.P., Hill,D.E., Iakoucheva,L.M.,
            Xia,Y. and Vidal,M.
  TITLE     Widespread Expansion of Protein Interaction Capabilities by
            Alternative Splicing
  JOURNAL   Cell 164 (4), 805-817 (2016)
   PUBMED   26871637
REFERENCE   5  (bases 1 to 2514)
  AUTHORS   Sahni,N., Yi,S., Taipale,M., Fuxman Bass,J.I.,
            Coulombe-Huntington,J., Yang,F., Peng,J., Weile,J., Karras,G.I.,
            Wang,Y., Kovacs,I.A., Kamburov,A., Krykbaeva,I., Lam,M.H.,
            Tucker,G., Khurana,V., Sharma,A., Liu,Y.Y., Yachie,N., Zhong,Q.,
            Shen,Y., Palagi,A., San-Miguel,A., Fan,C., Balcha,D., Dricot,A.,
            Jordan,D.M., Walsh,J.M., Shah,A.A., Yang,X., Stoyanova,A.K.,
            Leighton,A., Calderwood,M.A., Jacob,Y., Cusick,M.E.,
            Salehi-Ashtiani,K., Whitesell,L.J., Sunyaev,S., Berger,B.,
            Barabasi,A.L., Charloteaux,B., Hill,D.E., Hao,T., Roth,F.P.,
            Xia,Y., Walhout,A.J.M., Lindquist,S. and Vidal,M.
  TITLE     Widespread macromolecular interaction perturbations in human
            genetic disorders
  JOURNAL   Cell 161 (3), 647-660 (2015)
   PUBMED   25910212
REFERENCE   6  (bases 1 to 2514)
  AUTHORS   Li,Q., Wojciechowski,R., Simpson,C.L., Hysi,P.G., Verhoeven,V.J.,
            Ikram,M.K., Hohn,R., Vitart,V., Hewitt,A.W., Oexle,K., Makela,K.M.,
            MacGregor,S., Pirastu,M., Fan,Q., Cheng,C.Y., St Pourcain,B.,
            McMahon,G., Kemp,J.P., Northstone,K., Rahi,J.S., Cumberland,P.M.,
            Martin,N.G., Sanfilippo,P.G., Lu,Y., Wang,Y.X., Hayward,C.,
            Polasek,O., Campbell,H., Bencic,G., Wright,A.F., Wedenoja,J.,
            Zeller,T., Schillert,A., Mirshahi,A., Lackner,K., Yip,S.P.,
            Yap,M.K., Ried,J.S., Gieger,C., Murgia,F., Wilson,J.F., Fleck,B.,
            Yazar,S., Vingerling,J.R., Hofman,A., Uitterlinden,A.,
            Rivadeneira,F., Amin,N., Karssen,L., Oostra,B.A., Zhou,X.,
            Teo,Y.Y., Tai,E.S., Vithana,E., Barathi,V., Zheng,Y., Siantar,R.G.,
            Neelam,K., Shin,Y., Lam,J., Yonova-Doing,E., Venturini,C.,
            Hosseini,S.M., Wong,H.S., Lehtimaki,T., Kahonen,M., Raitakari,O.,
            Timpson,N.J., Evans,D.M., Khor,C.C., Aung,T., Young,T.L.,
            Mitchell,P., Klein,B., van Duijn,C.M., Meitinger,T., Jonas,J.B.,
            Baird,P.N., Mackey,D.A., Wong,T.Y., Saw,S.M., Parssinen,O.,
            Stambolian,D., Hammond,C.J., Klaver,C.C., Williams,C.,
            Paterson,A.D., Bailey-Wilson,J.E. and Guggenheim,J.A.
  CONSRTM   CREAM Consortium
  TITLE     Genome-wide association study for refractive astigmatism reveals
            genetic co-determination with spherical equivalent refractive
            error: the CREAM consortium
  JOURNAL   Hum Genet 134 (2), 131-146 (2015)
   PUBMED   25367360
REFERENCE   7  (bases 1 to 2514)
  AUTHORS   Winham,S.J., Cuellar-Barboza,A.B., Oliveros,A., McElroy,S.L.,
            Crow,S., Colby,C., Choi,D.S., Chauhan,M., Frye,M. and
            Biernacka,J.M.
  TITLE     Genome-wide association study of bipolar disorder accounting for
            effect of body mass index identifies a new risk allele in TCF7L2
  JOURNAL   Mol Psychiatry 19 (9), 1010-1016 (2014)
   PUBMED   24322204
REFERENCE   8  (bases 1 to 2514)
  AUTHORS   Reymond,A., Meroni,G., Fantozzi,A., Merla,G., Cairo,S., Luzi,L.,
            Riganelli,D., Zanaria,E., Messali,S., Cainarca,S., Guffanti,A.,
            Minucci,S., Pelicci,P.G. and Ballabio,A.
  TITLE     The tripartite motif family identifies cell compartments
  JOURNAL   EMBO J 20 (9), 2140-2151 (2001)
   PUBMED   11331580
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC397052.1, AF521868.1,
            AC026324.11 and BX093220.1.
            
            On Nov 22, 2018 this sequence version replaced NM_152616.4.
            
            Summary: This gene encodes a member of the tripartite motif (TRIM)
            family. The TRIM motif includes three zinc-binding domains, namely
            a RING, a B-box type 1 and a B-box type 2, and a coiled-coil
            region. [provided by RefSeq, Jul 2008].
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK097416.1, SRR5189667.196682.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2148093
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000286349.4/ ENSP00000286349.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-148               DC397052.1         41-188
            149-896             AF521868.1         1-748
            897-1205            AC026324.11        44411-44719         c
            1206-2338           AF521868.1         1058-2190
            2339-2514           BX093220.1         299-474
FEATURES             Location/Qualifiers
     source          1..2514
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q23"
     gene            1..2514
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /note="tripartite motif containing 42"
                     /db_xref="GeneID:287015"
                     /db_xref="HGNC:HGNC:19014"
                     /db_xref="MIM:620334"
     exon            1..507
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /inference="alignment:Splign:2.1.0"
     CDS             167..2338
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /note="protein phosphatase 1, regulatory subunit 40"
                     /codon_start=1
                     /product="tripartite motif-containing protein 42"
                     /protein_id="NP_689829.3"
                     /db_xref="CCDS:CCDS3113.1"
                     /db_xref="GeneID:287015"
                     /db_xref="HGNC:HGNC:19014"
                     /db_xref="MIM:620334"
                     /translation="METAMCVCCPCCTWQRCCPQLCSCLCCKFIFTSERNCTCFPCPY
                     KDERNCQFCHCTCSESPNCHWCCCSWANDPNCKCCCTASSNLNCYYYESRCCRNTIIT
                     FHKGRLRSIHTSSKTALRTGSSDTQVDEVKSIPANSHLVNHLNCPMCSRLRLHSFMLP
                     CNHSLCEKCLRQLQKHAEVTENFFILICPVCDRSHCMPYSNKMQLPENYLHGRLTKRY
                     MQEHGYLKWRFDRSSGPILCQVCRNKRIAYKRCITCRLNLCNDCLKAFHSDVAMQDHV
                     FVDTSAEEQDEKICIHHPSSRIIEYCRNDNKLLCTFCKFSFHNGHDTISLIDACSERA
                     ASLFSAIAKFKAVRYEIDNDLMEFNILKNSFKADKEAKRKEIRNGFLKLRSILQEKEK
                     IIMEQIENLEVSRQKEIEKYVYVTTMKVNEMDGLIAYSKEALKETGQVAFLQSAKILV
                     DQIEDGIQTTYRPDPQLRLHSINYVPLDFVELSSAIHELFPTGPKKVRSSGDSLPSPY
                     PVHSETMIARKVTFSTHSLGNQHIYQRSSSMLSFSNTDKKAKVGLEACGRAQSATPAK
                     PTDGLYTYWSAGADSQSVQNSSSFHNWYSFNDGSVKTPGPIVIYQTLVYPRAAKVYWT
                     CPAEDVDSFEMEFYEVITSPPNNVQMELCGQIRDIMQQNLELHNLTPNTEYVFKVRAI
                     NDNGPGQWSDICKVVTPDGHGKNRAKWGLLKNIQSALQKHF"
     exon            508..1205
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /inference="alignment:Splign:2.1.0"
     exon            1206..2026
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /inference="alignment:Splign:2.1.0"
     exon            2027..2251
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /inference="alignment:Splign:2.1.0"
     exon            2252..2514
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2496..2501
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /note="hexamer: AATAAA"
     polyA_site      2514
                     /gene="TRIM42"
                     /gene_synonym="PPP1R40; T4A1"
                     /note="major polyA site"
ORIGIN      
        1 agggacacca gctgtgaagt cctcataaca gccaacttct tgcaactttc aagctgacgg
       61 cctcaggaat gggaggaagg actcctccac tggagaactg atagcagtat tctggtagag
      121 gaggcatcaa gagtcctggg aggccggtgg taatcatgta ggcaccatgg aaactgctat
      181 gtgcgtttgc tgtccatgtt gtacatggca gagatgttgt cctcagttat gctcctgtct
      241 gtgctgcaag ttcatcttca cctcagagcg gaactgcacc tgcttcccct gcccttacaa
      301 agatgagcgg aactgccagt tctgccactg cacctgttct gagagcccca actgccattg
      361 gtgttgctgc tcttgggcca atgatcccaa ctgtaagtgc tgctgcacag ccagcagcaa
      421 tctcaactgc tactactatg agagccgctg ctgccgcaat accatcatca ctttccacaa
      481 gggccgcctc aggagcatcc atacctcctc caagactgcc ctgcgcactg ggagcagcga
      541 tacccaggtg gatgaagtaa agtcaatacc agccaacagt cacctggtga accacctcaa
      601 ttgccccatg tgcagccggc tgcgcctgca ctcattcatg ctgccctgca accacagcct
      661 gtgcgagaag tgcctgcggc agctgcagaa gcacgccgag gtcaccgaga acttcttcat
      721 cctcatctgc ccagtgtgcg accgctcgca ctgcatgccc tacagcaaca agatgcagct
      781 gcccgagaac tacctgcacg ggcgtctcac caagcgctac atgcaggagc acggctacct
      841 caagtggcgc tttgaccgct cctccgggcc catcctctgc caggtctgcc gcaacaagcg
      901 catcgcttac aagcgctgca tcacctgccg cctcaacctg tgcaacgact gcctcaaggc
      961 cttccactcg gatgtggcca tgcaagacca cgtctttgtg gacaccagcg ccgaggaaca
     1021 ggacgagaag atctgcatcc accacccatc cagccgcatc atcgagtact gccgcaatga
     1081 caacaaattg ctctgcacct tctgcaagtt ctctttccac aatggccacg acaccattag
     1141 cctcatcgac gcctgctccg agagggccgc ctcactcttc agcgccatcg ccaagttcaa
     1201 agcagtccga tatgaaattg ataatgacct aatggaattc aacatcttaa aaaacagctt
     1261 taaagctgac aaggaggcaa agcgaaaaga gatcagaaat ggctttctca agttgcgcag
     1321 cattcttcag gagaaagaga agatcatcat ggagcagata gagaatctag aagtgtccag
     1381 gcagaaggaa attgaaaaat atgtgtatgt tacaaccatg aaagtgaacg agatggatgg
     1441 tctgatcgcc tactccaagg aagccctgaa ggagactggc caggtggcat tcctgcagtc
     1501 agccaagatc ctggtggacc agatcgagga cggcatccag accacctaca ggcctgaccc
     1561 acagctccgg ctgcactcaa taaactacgt gcccttggac tttgttgagc tttccagtgc
     1621 catccatgag ctcttcccca cagggcccaa gaaggtacgc tcctcagggg actccctgcc
     1681 ctccccctac cccgtgcact cagaaacaat gattgccagg aaggtcactt tcagcaccca
     1741 cagcctcggc aaccagcaca tataccagcg aagctcctcc atgttgtcct tcagcaacac
     1801 tgacaagaag gccaaggtgg gtctggaggc ctgtgggaga gcccagtcag ccacccccgc
     1861 caaacccaca gacggcctct acacctactg gagtgctgga gcagacagcc agtctgtaca
     1921 gaacagcagc agcttccaca actggtactc attcaacgat ggctctgtga agaccccagg
     1981 cccaattgtt atctaccaga ctctggtgta cccaagagct gccaaggttt actggacatg
     2041 tccagcagaa gacgtggact cttttgagat ggaattctat gaagtcatta cttctcctcc
     2101 taacaacgta caaatggagc tctgtggaca aattcgggac ataatgcagc aaaatctgga
     2161 gctgcacaac ctgaccccca acacagaata cgtgtttaaa gttagagcca tcaatgataa
     2221 tggtcctggg caatggagtg atatctgcaa ggtggtaaca ccagatggac atgggaagaa
     2281 ccgagctaag tggggcctgc tgaagaatat ccagtctgcc ctccagaagc acttctgagc
     2341 cccttcagag caggaaacaa cctcagactc atcacaaagt agacatatac acacacatat
     2401 atgtatgtat atttttctca ccacattctt caaggaggtt gtagacaaat gtttccatga
     2461 cctctcagct ttccaacagg aatcttgtaa gagctaataa aaggaaatac ctga
//
