LOCUS       NM_001369521            3166 bp    mRNA    linear   PRI 22-SEP-2024
DEFINITION  Homo sapiens tripartite motif containing 39 (TRIM39), transcript
            variant 3, mRNA.
ACCESSION   NM_001369521
VERSION     NM_001369521.2
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 3166)
  AUTHORS   Ogura,T., Azuma,K., Takeiwa,T., Sato,J., Kinowaki,K., Ikeda,K.,
            Kawabata,H. and Inoue,S.
  TITLE     TRIM39 is a poor prognostic factor for patients with estrogen
            receptor-positive breast cancer and promotes cell cycle progression
  JOURNAL   Pathol Int 72 (2), 96-106 (2022)
   PUBMED   35174936
  REMARK    GeneRIF: TRIM39 is a poor prognostic factor for patients with
            estrogen receptor-positive breast cancer and promotes cell cycle
            progression.
REFERENCE   2  (bases 1 to 3166)
  AUTHORS   Hu,J., Ding,X., Tian,S., Chu,Y., Liu,Z., Li,Y., Li,X., Wang,G.,
            Wang,L. and Wang,Z.
  TITLE     TRIM39 deficiency inhibits tumor progression and autophagic flux in
            colorectal cancer via suppressing the activity of Rab7
  JOURNAL   Cell Death Dis 12 (4), 391 (2021)
   PUBMED   33846303
  REMARK    GeneRIF: TRIM39 deficiency inhibits tumor progression and
            autophagic flux in colorectal cancer via suppressing the activity
            of Rab7.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3166)
  AUTHORS   Ning,L., Ko,J.M., Yu,V.Z., Ng,H.Y., Chan,C.K., Tao,L., Lam,S.Y.,
            Leong,M.M., Ngan,R.K., Kwong,D.L., Lee,A.W., Ng,W.T., Cheng,A.,
            Tung,S., Lee,V.H., Lam,K.O., Kwan,C.K., Li,W.S., Yau,S., Bei,J.X.
            and Lung,M.L.
  TITLE     Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA
            and novel non-HLA TRIM31 and TRIM39 loci
  JOURNAL   Commun Biol 3 (1), 759 (2020)
   PUBMED   33311639
  REMARK    GeneRIF: Nasopharyngeal carcinoma MHC region deep sequencing
            identifies HLA and novel non-HLA TRIM31 and TRIM39 loci.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3166)
  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   5  (bases 1 to 3166)
  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 3166)
  AUTHORS   Roberts,J.D. Jr., Chiche,J.D., Kolpa,E.M., Bloch,D.B. and
            Bloch,K.D.
  TITLE     cGMP-dependent protein kinase I interacts with TRIM39R, a novel
            Rpp21 domain-containing TRIM protein
  JOURNAL   Am J Physiol Lung Cell Mol Physiol 293 (4), L903-L912 (2007)
   PUBMED   17601797
REFERENCE   7  (bases 1 to 3166)
  AUTHORS   Wu,C., Ma,M.H., Brown,K.R., Geisler,M., Li,L., Tzeng,E., Jia,C.Y.,
            Jurisica,I. and Li,S.S.
  TITLE     Systematic identification of SH3 domain-mediated human
            protein-protein interactions by peptide array target screening
  JOURNAL   Proteomics 7 (11), 1775-1785 (2007)
   PUBMED   17474147
REFERENCE   8  (bases 1 to 3166)
  AUTHORS   Tao,W.A., Wollscheid,B., O'Brien,R., Eng,J.K., Li,X.J.,
            Bodenmiller,B., Watts,J.D., Hood,L. and Aebersold,R.
  TITLE     Quantitative phosphoproteome analysis using a dendrimer conjugation
            chemistry and tandem mass spectrometry
  JOURNAL   Nat Methods 2 (8), 591-598 (2005)
   PUBMED   16094384
REFERENCE   9  (bases 1 to 3166)
  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
REFERENCE   10 (bases 1 to 3166)
  AUTHORS   Orimo,A., Yamagishi,T., Tominaga,N., Yamauchi,Y., Hishinuma,T.,
            Okada,K., Suzuki,M., Sato,M., Nogi,Y., Suzuki,H., Inoue,S.,
            Yoshimura,K., Shimizu,Y. and Muramatsu,M.
  TITLE     Molecular cloning of testis-abundant finger Protein/Ring finger
            protein 23 (RNF23), a novel RING-B box-coiled coil-B30.2 protein on
            the class I region of the human MHC
  JOURNAL   Biochem Biophys Res Commun 276 (1), 45-51 (2000)
   PUBMED   11006080
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL662795.5.
            
            On Jun 9, 2021 this sequence version replaced NM_001369521.1.
            
            Summary: The protein encoded by this gene is a member of the
            tripartite motif (TRIM) family. The TRIM motif includes three
            zinc-binding domains, a RING, a B-box type 1 and a B-box type 2,
            and a coiled-coil region. The function of this protein has not been
            identified. This gene lies within the major histocompatibility
            complex class I region on chromosome 6. Alternate splicing results
            in two transcript variants encoding different isoforms. [provided
            by RefSeq, Jul 2008].
            
            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 :: SRR14038192.2552948.1,
                                           SRR18074969.1177246.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000396551.9/ ENSP00000379800.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-69                AL662795.5         60280-60348
            70-222              AL662795.5         62242-62394
            223-682             AL662795.5         62664-63123
            683-778             AL662795.5         64134-64229
            779-1009            AL662795.5         69098-69328
            1010-1032           AL662795.5         73261-73283
            1033-1148           AL662795.5         73858-73973
            1149-3166           AL662795.5         75065-77082
FEATURES             Location/Qualifiers
     source          1..3166
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p22.1"
     gene            1..3166
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /note="tripartite motif containing 39"
                     /db_xref="GeneID:56658"
                     /db_xref="HGNC:HGNC:10065"
                     /db_xref="MIM:605700"
     exon            1..69
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /inference="alignment:Splign:2.1.0"
     exon            70..222
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /inference="alignment:Splign:2.1.0"
     exon            223..682
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /inference="alignment:Splign:2.1.0"
     CDS             230..1696
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /EC_number="2.3.2.27"
                     /note="isoform 2 is encoded by transcript variant 3; ring
                     finger protein 23; testis-abundant finger protein;
                     tripartite motif-containing protein 39; E3
                     ubiquitin-protein ligase TRIM39; RING-type E3 ubiquitin
                     transferase TRIM39"
                     /codon_start=1
                     /product="E3 ubiquitin-protein ligase TRIM39 isoform 2"
                     /protein_id="NP_001356450.1"
                     /db_xref="CCDS:CCDS34378.1"
                     /db_xref="GeneID:56658"
                     /db_xref="HGNC:HGNC:10065"
                     /db_xref="MIM:605700"
                     /translation="MAETSLLEAGASAASTAAALENLQVEASCSVCLEYLKEPVIIEC
                     GHNFCKACITRWWEDLERDFPCPVCRKTSRYRSLRPNRQLGSMVEIAKQLQAVKRKIR
                     DESLCPQHHEALSLFCYEDQEAVCLICAISHTHRAHTVVPLDDATQEYKEKLQKCLEP
                     LEQKLQEITRCKSSEEKKPGELKRLVESRRQQILREFEELHRRLDEEQQVLLSRLEEE
                     EQDILQRLRENAAHLGDKRRDLAHLAAEVEGKCLQSGFEMLKDVKSTLEKCEKVKTME
                     VTSVSIELEKNFSNFPRQYFALRKILKQLIADVTLDPETAHPNLVLSEDRKSVKFVET
                     RLRDLPDTPRRFTFYPCVLATEGFTSGRHYWEVEVGDKTHWAVGVCRDSVSRKGELTP
                     LPETGYWRVRLWNGDKYAATTTPFTPLHIKVKPKRVGIFLDYEAGTLSFYNVTDRSHI
                     YTFTDTFTEKLWPLFYPGIRAGRKNAAPLTIRPPTDWE"
     exon            683..778
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /inference="alignment:Splign:2.1.0"
     exon            779..1009
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /inference="alignment:Splign:2.1.0"
     exon            1010..1032
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /inference="alignment:Splign:2.1.0"
     exon            1033..1148
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /inference="alignment:Splign:2.1.0"
     exon            1149..3166
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3145..3150
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /note="hexamer: AACAAA"
     polyA_site      3166
                     /gene="TRIM39"
                     /gene_synonym="RNF23; TFP; TRIM39B"
                     /note="major polyA site"
ORIGIN      
        1 gaggaggaag gagggaggca gcgctccggc ggctccgcgc cccgcactcc cggacccgaa
       61 gccgggaaga ttcctttctt gtctgttaga aacgtatgtc aaacgaggat acagtgtctg
      121 gaactattgg ttctaagata taagtggaat gagcctggat caggagaagt atgctgagct
      181 agagttgaag gaagcttctc tttctaacaa gagaaagcag agttaaatta tggcagagac
      241 aagtctgtta gaggctgggg cctctgcagc ctctacagct gcggctttgg agaacttaca
      301 ggtggaggcg agctgctctg tgtgcctgga gtatctgaag gaacctgtca tcattgagtg
      361 tgggcacaac ttctgcaaag cttgcatcac ccgctggtgg gaggacctag agagggactt
      421 cccttgtcct gtctgtcgaa agacatcccg ctaccgcagt ctccgaccta atcggcaact
      481 aggcagtatg gtggaaattg ccaagcagct ccaggccgtc aagcggaaga tccgggatga
      541 gagcctctgc ccccaacacc atgaggccct cagccttttc tgttatgagg accaggaggc
      601 tgtatgcttg atatgtgcaa tttcccacac ccaccgggcc cacaccgttg tgccactgga
      661 cgatgctaca caggagtaca aggaaaaact gcagaagtgt ctggagcccc tggaacagaa
      721 gctgcaggag atcactcgct gcaagtcctc tgaggagaag aagcctggtg agctcaagag
      781 actagtggaa agtcgccgac agcagatctt gagggagttt gaagagcttc ataggcggct
      841 ggatgaagag cagcaggtgt tgctttcacg actggaagaa gaggaacagg acattctgca
      901 gcgactccga gaaaatgctg ctcaccttgg ggacaagcgc cgggacctgg cccacttggc
      961 tgccgaggtg gagggcaagt gcttacagtc aggcttcgag atgcttaagg atgtcaaaag
     1021 taccctggaa aaatgtgaaa aggtgaagac catggaggtg acttcagtat ccatagagct
     1081 ggaaaagaac ttcagcaatt ttccccgaca gtactttgcc ctaaggaaaa tccttaaaca
     1141 gctaattgcg gatgtgaccc tggaccctga gacagctcat cctaacctag tcctgtcaga
     1201 ggatcgtaag agcgtcaagt tcgtggagac aagactccgg gatctccctg acacaccaag
     1261 gcgtttcacc ttctaccctt gcgtcctggc tactgagggt ttcacctcag gtcgacacta
     1321 ctgggaggtg gaggtgggcg acaagaccca ctgggcagtg ggtgtatgcc gggactccgt
     1381 gagccgaaag ggcgagttga ctccactccc tgagactggc tactggcggg tgcggctatg
     1441 gaatggggac aaatatgcag ccaccaccac accttttacc cctttgcaca tcaaggtgaa
     1501 acccaagcgg gtaggcatat tcctagacta tgaggccggc acactgtctt tctacaatgt
     1561 cacagaccgc tctcatatct acaccttcac tgatactttt actgagaaac tttggcccct
     1621 cttctaccca ggcatccggg ctggacggaa gaatgctgca ccacttacca tcaggccccc
     1681 aacagattgg gagtgacagg ttgggatgtg ggaatgactg gggtgaggca gggtcaagtg
     1741 ctacgggcct ccttcccgtg tcctgctgga acgtcttcgt gtccacctgg gtccagtcct
     1801 gaatcatctt ggagaaacac cttggtttct aggatggttt tgtgtggagg gggaggtagg
     1861 actgggctgg atgagagagc acagctgtga cttcctccta actgtcaggg tggggagctg
     1921 gttcccagag gattgtctac cctgaagtcc atcaggtttt ctgttgcaca aggacgggtc
     1981 aggaaggaag gagaggcttt tccagaaaca aaaaatctgt gagggtctga cttgctcaaa
     2041 ccagaggagg aaacagaaac ccctgcacat ctttttaggg ggttctttga cccaggatag
     2101 tcttgcttct tgaggtagat cacaggggtc tgtgtacctc tgaattcatg agagatgaat
     2161 gacagatgct ctcatgggtc tagatattga ggagtttttc tgagggcaga gattggacat
     2221 caacaaggct agaagggtca gggaagtggg ctaaaggaac agattcctag agattaatga
     2281 agaggaggga ggtttctttg gtcttctatt ccaagggtaa ggttgcgatt atgggtaaga
     2341 ttggccagag gtaggaatgt ggggagaagg agaggctgaa aagaaagcag aggagaaccc
     2401 aggtccctgc ctcagccttc agcagagttg gcttattgcc tgcctctata ccaataagtc
     2461 agtcaccttg ctcctctcca gaggcaaagt ggaagagatc ctgcaagaca catctatcct
     2521 ttcacagtgt tcccaaggga acttggaaag gagagtcagg tattagagga aagagaaggg
     2581 tatttgtata caaagccctg gccttaaaga atgttactta gtagctactc ccaaattgtc
     2641 agccttctta cctggccaag gtgtccaagc cagaaaggaa aaaaggttat ggagtctttc
     2701 tcaccctaag gacagggtgg aagagggtgg tatataggga agggccagat aggcaacttc
     2761 atttggcttg tgtgcatctg gcctggaact ggtgttaagc caggcttttg cttgtttgtt
     2821 gccatccctc accctttgcc atttcccttt tcagagaatg taaatgattt tcatgttagg
     2881 ccaaaataaa caacttatag ggtacatatg ttgtcataaa aggtaaaagt gatgcatgcc
     2941 aaaccaaact aaaccaattt ggattatctg ctattcgggt aatcttcaca gaaatgactg
     3001 agagaagaat ctgcagttta ctgagggcat ttcagttcct cctaccacct caacaggact
     3061 ttgtccagac tctcctcctc ttacctttgt gccttgactg tggttctttg tggcaagata
     3121 ctttggttgg ttaaaataat atggaacaaa ggatccactg aagtga
//
