LOCUS       NM_022727               2886 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens tRNA methyltransferase 2 homolog A (TRMT2A),
            transcript variant 1, mRNA.
ACCESSION   NM_022727
VERSION     NM_022727.6
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 2886)
  AUTHORS   Witzenberger,M., Burczyk,S., Settele,D., Mayer,W., Welp,L.M.,
            Heiss,M., Wagner,M., Monecke,T., Janowski,R., Carell,T., Urlaub,H.,
            Hauck,S.M., Voigt,A. and Niessing,D.
  TITLE     Human TRMT2A methylates tRNA and contributes to translation
            fidelity
  JOURNAL   Nucleic Acids Res 51 (16), 8691-8710 (2023)
   PUBMED   37395448
  REMARK    GeneRIF: Human TRMT2A methylates tRNA and contributes to
            translation fidelity.
REFERENCE   2  (bases 1 to 2886)
  AUTHORS   Dai,W., Li,A., Yu,N.J., Nguyen,T., Leach,R.W., Wuhr,M. and
            Kleiner,R.E.
  TITLE     Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated
            dihydrouridylation
  JOURNAL   Nat Chem Biol 17 (11), 1178-1187 (2021)
   PUBMED   34556860
REFERENCE   3  (bases 1 to 2886)
  AUTHORS   Pereira,M., Ribeiro,D.R., Pinheiro,M.M., Ferreira,M., Kellner,S.
            and Soares,A.R.
  TITLE     m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation
            of tRNA-Derived Small RNAs
  JOURNAL   Int J Mol Sci 22 (6), 2941 (2021)
   PUBMED   33799331
  REMARK    GeneRIF: m(5)U54 tRNA Hypomodification by Lack of TRMT2A Drives the
            Generation of tRNA-Derived Small RNAs.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2886)
  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 2886)
  AUTHORS   Cheng,Q.Y., Xiong,J., Ma,C.J., Dai,Y., Ding,J.H., Liu,F.L.,
            Yuan,B.F. and Feng,Y.Q.
  TITLE     Chemical tagging for sensitive determination of uridine
            modifications in RNA
  JOURNAL   Chem Sci 11 (7), 1878-1891 (2020)
   PUBMED   34123281
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2886)
  AUTHORS   Hicks,D.G., Janarthanan,B.R., Vardarajan,R., Kulkarni,S.A.,
            Khoury,T., Dim,D., Budd,G.T., Yoder,B.J., Tubbs,R., Schreeder,M.T.,
            Estopinal,N.C., Beck,R.A., Wang,Y., Ring,B.Z., Seitz,R.S. and
            Ross,D.T.
  TITLE     The expression of TRMT2A, a novel cell cycle regulated protein,
            identifies a subset of breast cancer patients with HER2
            over-expression that are at an increased risk of recurrence
  JOURNAL   BMC Cancer 10, 108 (2010)
   PUBMED   20307320
  REMARK    GeneRIF: TRMT2A staining showed a strong correlation with
            likelihood of recurrence at five years in 67 HER2+ breast cancer.
            Publication Status: Online-Only
REFERENCE   7  (bases 1 to 2886)
  AUTHORS   Liu,Y.L., Fann,C.S., Liu,C.M., Chang,C.C., Yang,W.C., Wu,J.Y.,
            Hung,S.I., Chan,H.Y., Chen,J.J., Hsieh,M.H., Hwang,T.J.,
            Faraone,S.V., Tsuang,M.T., Chen,W.J. and Hwu,H.G.
  TITLE     HTF9C gene of 22q11.21 region associates with schizophrenia having
            deficit-sustained attention
  JOURNAL   Psychiatr Genet 17 (6), 333-338 (2007)
   PUBMED   18075473
  REMARK    GeneRIF: Single nucleotid polymorphisms of this gene may be
            associated with a deficit in sustained attention within
            schizophrenia, in a Taiwanese cohort.
            GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 2886)
  AUTHORS   Collins,J.E., Wright,C.L., Edwards,C.A., Davis,M.P., Grinham,J.A.,
            Cole,C.G., Goward,M.E., Aguado,B., Mallya,M., Mokrab,Y.,
            Huckle,E.J., Beare,D.M. and Dunham,I.
  TITLE     A genome annotation-driven approach to cloning the human ORFeome
  JOURNAL   Genome Biol 5 (10), R84 (2004)
   PUBMED   15461802
REFERENCE   9  (bases 1 to 2886)
  AUTHORS   Dunham,I., Shimizu,N., Roe,B.A., Chissoe,S., Hunt,A.R.,
            Collins,J.E., Bruskiewich,R., Beare,D.M., Clamp,M., Smink,L.J.,
            Ainscough,R., Almeida,J.P., Babbage,A., Bagguley,C., Bailey,J.,
            Barlow,K., Bates,K.N., Beasley,O., Bird,C.P., Blakey,S.,
            Bridgeman,A.M., Buck,D., Burgess,J., Burrill,W.D., O'Brien,K.P. et
            al.
  TITLE     The DNA sequence of human chromosome 22
  JOURNAL   Nature 402 (6761), 489-495 (1999)
   PUBMED   10591208
  REMARK    Erratum:[Nature 2000 Apr 20;404(6780):904]
REFERENCE   10 (bases 1 to 2886)
  AUTHORS   Di Matteo,G., Salerno,M., Guarguaglini,G., Di Fiore,B., Palitti,F.
            and Lavia,P.
  TITLE     Interactions with single-stranded and double-stranded DNA-binding
            factors and alternative promoter conformation upon transcriptional
            activation of the Htf9-a/RanBP1 and Htf9-c genes
  JOURNAL   J Biol Chem 273 (1), 495-505 (1998)
   PUBMED   9417108
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BX349795.2, AC006547.9,
            BC017184.2 and AI539558.1.
            
            On Nov 23, 2018 this sequence version replaced NM_022727.5.
            
            Summary: The protein encoded by this gene is of unknown function.
            However, it is orthologous to the mouse Trmt2a gene and contains an
            RNA methyltransferase domain. Expression of this gene varies during
            the cell cycle, with aberrant expression being a possible biomarker
            in certain breast cancers. Several transcript variants encoding two
            different isoforms have been found for this gene. [provided by
            RefSeq, Apr 2012].
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (a). Variants 1 and 2 both encode the same isoform (a).
            
            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 :: BC108251.1, CR456354.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000252136.12/ ENSP00000252136.7
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-55                BX349795.2         70-124
            56-56               AC006547.9         78202-78202         c
            57-160              BX349795.2         125-228
            161-161             AC006547.9         78097-78097         c
            162-210             BX349795.2         229-277
            211-344             AC006547.9         77914-78047         c
            345-919             AC006547.9         77069-77643         c
            920-1028            AC006547.9         76703-76811         c
            1029-1210           AC006547.9         76297-76478         c
            1211-1325           AC006547.9         75996-76110         c
            1326-1441           AC006547.9         75792-75907         c
            1442-1553           AC006547.9         75605-75716         c
            1554-1676           AC006547.9         74717-74839         c
            1677-1752           AC006547.9         74463-74538         c
            1753-1869           AC006547.9         74149-74265         c
            1870-1966           AC006547.9         73942-74038         c
            1967-2300           AC006547.9         73492-73825         c
            2301-2629           BC017184.2         2132-2460
            2630-2886           AI539558.1         13-269              c
FEATURES             Location/Qualifiers
     source          1..2886
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="22"
                     /map="22q11.21"
     gene            1..2886
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /note="tRNA methyltransferase 2 homolog A"
                     /db_xref="GeneID:27037"
                     /db_xref="HGNC:HGNC:24974"
                     /db_xref="MIM:611151"
     exon            1..344
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     CDS             321..2198
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /EC_number="2.1.1.35"
                     /note="isoform a is encoded by transcript variant 1; tRNA
                     (uracil-5-)-methyltransferase homolog A; hpaII tiny
                     fragments locus 9c protein; TRM2 tRNA methyltransferase 2
                     homolog A; mRNA (uracil-5-)-methyltransferase TRMT2A"
                     /codon_start=1
                     /product="tRNA (uracil-5-)-methyltransferase homolog A
                     isoform a"
                     /protein_id="NP_073564.3"
                     /db_xref="CCDS:CCDS13774.1"
                     /db_xref="GeneID:27037"
                     /db_xref="HGNC:HGNC:24974"
                     /db_xref="MIM:611151"
                     /translation="MSENLDNEGPKPMESCGQESSSALSCPTVSVPPAAPAALEEVEK
                     EGAGAATGPGPQPGLYSYIRDDLFTSEIFKLELQNVPRHASFSDVRRFLGRFGLQPHK
                     TKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGRPLSVRLARPKADPMARRRRQEGE
                     SEPPVTRVADVVTPLWTVPYAEQLERKQLECEQVLQKLAKEIGSTNRALLPWLLEQRH
                     KHNKACCPLEGVRPSPQQTEYRNKCEFLVGVGVDGEDNTVGCRLGKYKGGTCAVAAPF
                     DTVHIPEATKQVVKAFQEFIRSTPYSAYDPETYTGHWKQLTVRTSRRHQAMAIAYFHP
                     QKLSPEELAELKTSLAQHFTAGPGRASGVTCLYFVEEGQRKTPSQEGLPLEHVAGDRC
                     IHEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLAL
                     ARKVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRAEDLVPTLVSRLASQHLVAI
                     LDPPRAGLHSKVILAIRRAKNLRRLLYVSCNPRAAMGNFVDLCRAPSNRVKGIPFRPV
                     KAVAVDLFPQTPHCEMLILFERVEHPNGTGVLGPHSPPAQPTPGPPDNTLQETGTFPS
                     S"
     exon            345..919
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            920..1028
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1029..1210
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1211..1325
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1326..1441
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1442..1553
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1554..1676
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1677..1752
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1753..1869
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1870..1966
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     exon            1967..2886
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2440..2445
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /note="hexamer: AATAAA"
     polyA_site      2460
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /note="major polyA site"
     regulatory      2867..2872
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
                     /note="hexamer: AATAAA"
     polyA_site      2886
                     /gene="TRMT2A"
                     /gene_synonym="HTF9C"
ORIGIN      
        1 atagagacgc tcggcctccg ccgcacgcgc tggcggacta agagtggctg gcgaagcgag
       61 cggccggcgc gggcccctgg cgggcgggcg gtacagcccc aagcctgaga cccggacctg
      121 agcatcgcag gttcgagtcc cgccccgcct ggggcgaagc cgggggtggc ggcgacctcg
      181 cggcgttgca ccggctctgt gagcacctcc cctctgagca cttcccttgt gacaggccac
      241 ttcccttgtg acaggcccag gacgaggtgg ccaggcggcc cccatggcgt ccctggtcta
      301 ggcggagaac cgcctgggcg atgagtgaga acctcgacaa cgagggcccg aagcccatgg
      361 agagctgtgg ccaggagagc agcagtgccc tgagctgccc taccgtctcg gtgccccctg
      421 cagccccggc agccctggag gaggtggaga aagagggcgc tggggcggct acagggccgg
      481 ggcctcagcc cgggctctac agctacatca gggatgactt gtttacctct gagatcttta
      541 aactggagct gcagaacgtg cctcgccacg ccagcttcag cgacgtccgg cgcttcctgg
      601 gccgctttgg tctgcagccc cacaaaacca aactctttgg gcaaccaccc tgcgcctttg
      661 tgacattccg cagcgctgca gagagggaca aggccctgcg cgttttgcat ggtgccctct
      721 ggaaaggccg cccactcagt gtgcgcctgg cccggcccaa ggccgacccc atggccagga
      781 ggaggcgaca ggagggtgag agtgagccac cagtaacacg agtggccgac gtggtgaccc
      841 ctctatggac agtgccctat gctgagcagc ttgagcggaa gcagctggag tgcgagcagg
      901 tgctgcagaa acttgccaag gaaatcggga gcaccaaccg tgccttgctg ccctggctgc
      961 tcgagcagag gcacaagcac aacaaggcct gctgcccgct ggagggggtc aggccatcac
     1021 cccagcagac tgagtatcgt aataagtgtg agtttctggt tggcgtcggg gtggatgggg
     1081 aggataacac cgtgggctgt cggctcggca agtacaaggg cgggacgtgt gctgtggcag
     1141 ccccgtttga caccgtgcac atccccgaag ccaccaagca ggtggtgaag gccttccagg
     1201 agttcatccg gtccactcca tactcggcat acgacccaga gacgtacaca ggccactgga
     1261 agcagctgac tgtgcgcacc agccgccgcc accaggccat ggccattgcc tacttccacc
     1321 cccagaagct gagccctgag gagctggcag agctgaagac ctccctagcg cagcacttca
     1381 cagcagggcc aggcagggcc agtggagtga cctgcctcta cttcgtggag gagggacagc
     1441 gaaagactcc tagccaggag ggcctgcccc tggagcatgt ggctggggac cggtgcatcc
     1501 acgaggacct gctagggctg accttccgga tctctccaca cgccttcttc caggtgaaca
     1561 cacccgcagc cgaggtgctc tacacagtca tccaggactg ggcccaattg gatgcgggga
     1621 gcatggtgct ggacgtgtgc tgtggcaccg gcaccattgg cctggccctg gcccggaagg
     1681 taaagagggt cattggggtc gagctatgcc cagaggctgt ggaggacgcc cgggtgaacg
     1741 cccaggacaa tgagttgagt aatgtggagt tccactgcgg gagggccgag gacctggtgc
     1801 ccaccctggt gagcagactg gcctcccagc acctcgtggc catcctggac ccaccccgtg
     1861 ctggcttgca ttccaaggtg atcctggcca tccggagagc taagaacctc aggcggctgc
     1921 tgtacgtctc atgcaacccc cgggcagcca tgggcaactt tgtggacctc tgcagagccc
     1981 catctaaccg ggtgaagggc attcccttcc ggccggtcaa ggctgtggca gtggacctgt
     2041 tcccgcagac cccgcactgt gagatgctca tcctgtttga gagggtggag caccccaatg
     2101 gcacaggggt cttggggccc cacagccctc cagctcaacc cacaccagga cccccagata
     2161 acaccctaca agaaactggg accttcccct catcctaggc ccaggaccca ttatggggac
     2221 aggagctgaa gggctcccag ggccccaggg gcggggaagg catggcttgc tggccaggat
     2281 attcagaggt aggcagccaa agggcacaga accctgtgcc ccaccaggat tggcctgctg
     2341 ctaggggcca ggggccctga ccaggaagac aggtgggttc ctgtagcctg ttgcccatcc
     2401 ccagggcctt tgtggactag ccaaggctgt gagggccaga ataaacaact gctcaacaaa
     2461 gggtgtttct gtgatgagag ccaggggtct gaacacaggg cctgggtgcc agggaaaggg
     2521 ccaaactagg cctaggcagc tctgcaagcc tctctgcatg gctgggggag tcagggcaga
     2581 gcttacttta aaaaagaatg ttcgatttga tacttaaact tgaggagagg cagagagagg
     2641 tctgggaact gcaccagctg ggggcatggg gtggagaaca ctgggcagag ttggcccctc
     2701 tgtggccagc ctggccctca gcccagcaga gagggcatca accaaggaag gggccatgct
     2761 ggggtgctgc tcagctgtta caaaggcagg gtccagcctg cagggaggcc ccaggagggg
     2821 atctggccag tcaagggtcc acagggtgcc agcctctcac cctcagaata aagacatcag
     2881 ccattc
//
