LOCUS       NM_001080999            3637 bp    mRNA    linear   ROD 09-FEB-2025
DEFINITION  Mus musculus TRM2 tRNA methyltransferase 2A (Trmt2a), transcript
            variant 2, mRNA.
ACCESSION   NM_001080999
VERSION     NM_001080999.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3637)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 3637)
  AUTHORS   Ingham,N.J., Pearson,S.A., Vancollie,V.E., Rook,V., Lewis,M.A.,
            Chen,J., Buniello,A., Martelletti,E., Preite,L., Lam,C.C.,
            Weiss,F.D., Powis,Z., Suwannarat,P., Lelliott,C.J., Dawson,S.J.,
            White,J.K. and Steel,K.P.
  TITLE     Mouse screen reveals multiple new genes underlying mouse and human
            hearing loss
  JOURNAL   PLoS Biol 17 (4), e3000194 (2019)
   PUBMED   30973865
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3637)
  AUTHORS   Dickinson,M.E., Flenniken,A.M., Ji,X., Teboul,L., Wong,M.D.,
            White,J.K., Meehan,T.F., Weninger,W.J., Westerberg,H., Adissu,H.,
            Baker,C.N., Bower,L., Brown,J.M., Caddle,L.B., Chiani,F., Clary,D.,
            Cleak,J., Daly,M.J., Denegre,J.M., Doe,B., Dolan,M.E., Edie,S.M.,
            Fuchs,H., Gailus-Durner,V., Galli,A., Gambadoro,A., Gallegos,J.,
            Guo,S., Horner,N.R., Hsu,C.W., Johnson,S.J., Kalaga,S., Keith,L.C.,
            Lanoue,L., Lawson,T.N., Lek,M., Mark,M., Marschall,S., Mason,J.,
            McElwee,M.L., Newbigging,S., Nutter,L.M., Peterson,K.A.,
            Ramirez-Solis,R., Rowland,D.J., Ryder,E., Samocha,K.E.,
            Seavitt,J.R., Selloum,M., Szoke-Kovacs,Z., Tamura,M., Trainor,A.G.,
            Tudose,I., Wakana,S., Warren,J., Wendling,O., West,D.B., Wong,L.,
            Yoshiki,A., MacArthur,D.G., Tocchini-Valentini,G.P., Gao,X.,
            Flicek,P., Bradley,A., Skarnes,W.C., Justice,M.J., Parkinson,H.E.,
            Moore,M., Wells,S., Braun,R.E., Svenson,K.L., de Angelis,M.H.,
            Herault,Y., Mohun,T., Mallon,A.M., Henkelman,R.M., Brown,S.D.,
            Adams,D.J., Lloyd,K.C., McKerlie,C., Beaudet,A.L., Bucan,M. and
            Murray,S.A.
  CONSRTM   International Mouse Phenotyping Consortium; Jackson Laboratory;
            Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris
            (ICS); Charles River Laboratories; MRC Harwell; Toronto Centre for
            Phenogenomics; Wellcome Trust Sanger Institute; RIKEN BioResource
            Center
  TITLE     High-throughput discovery of novel developmental phenotypes
  JOURNAL   Nature 537 (7621), 508-514 (2016)
   PUBMED   27626380
  REMARK    Erratum:[Nature. 2017 Nov 16;551(7680):398. doi:
            10.1038/nature24643.. PMID: 29144450]
REFERENCE   4  (bases 1 to 3637)
  AUTHORS   Paronett,E.M., Meechan,D.W., Karpinski,B.A., LaMantia,A.S. and
            Maynard,T.M.
  TITLE     Ranbp1, Deleted in DiGeorge/22q11.2 Deletion Syndrome, is a
            Microcephaly Gene That Selectively Disrupts Layer 2/3 Cortical
            Projection Neuron Generation
  JOURNAL   Cereb Cortex 25 (10), 3977-3993 (2015)
   PUBMED   25452572
REFERENCE   5  (bases 1 to 3637)
  AUTHORS   Karpinski,B.A., Maynard,T.M., Fralish,M.S., Nuwayhid,S., Zohn,I.E.,
            Moody,S.A. and LaMantia,A.S.
  TITLE     Dysphagia and disrupted cranial nerve development in a mouse model
            of DiGeorge (22q11) deletion syndrome
  JOURNAL   Dis Model Mech 7 (2), 245-257 (2014)
   PUBMED   24357327
REFERENCE   6  (bases 1 to 3637)
  AUTHORS   Stapleton,G., Somma,M.P. and Lavia,P.
  TITLE     Cell type-specific interactions of transcription factors with a
            housekeeping promoter in vivo
  JOURNAL   Nucleic Acids Res 21 (10), 2465-2471 (1993)
   PUBMED   8389443
REFERENCE   7  (bases 1 to 3637)
  AUTHORS   Tyndall,C., Watt,F., Molloy,P.L., Vincent,P.C. and Frommer,M.
  TITLE     Binding of proteins from embryonic and differentiated cells to a
            bidirectional promoter contained within a CpG island
  JOURNAL   J Mol Biol 226 (2), 289-299 (1992)
   PUBMED   1640448
REFERENCE   8  (bases 1 to 3637)
  AUTHORS   Bressan,A., Somma,M.P., Lewis,J., Santolamazza,C., Copeland,N.G.,
            Gilbert,D.J., Jenkins,N.A. and Lavia,P.
  TITLE     Characterization of the opposite-strand genes from the mouse
            bidirectionally transcribed HTF9 locus
  JOURNAL   Gene 103 (2), 201-209 (1991)
   PUBMED   1889746
REFERENCE   9  (bases 1 to 3637)
  AUTHORS   Lavia,P., Macleod,D. and Bird,A.
  TITLE     Coincident start sites for divergent transcripts at a randomly
            selected CpG-rich island of mouse
  JOURNAL   EMBO J 6 (9), 2773-2779 (1987)
   PUBMED   2445562
REFERENCE   10 (bases 1 to 3637)
  AUTHORS   Bird,A., Taggart,M., Frommer,M., Miller,O.J. and Macleod,D.
  TITLE     A fraction of the mouse genome that is derived from islands of
            nonmethylated, CpG-rich DNA
  JOURNAL   Cell 40 (1), 91-99 (1985)
   PUBMED   2981636
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AK134368.1, AC084822.36 and AK080170.1.
            
            On Aug 26, 2010 this sequence version replaced NM_001080999.1.
            
            Transcript Variant: This variant (2) lacks a segment of the 5' UTR
            and 5' coding region, and uses an upstream start codon, compared to
            variant 1. The resulting isoform (2) has a distinct N-terminus and
            is the same length as isoform 1.
            
            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.
            
            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 :: AK134368.1, AK151422.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2362              AK134368.1         2-2363
            2363-2761           AC084822.36        52940-53338
            2762-3637           AK080170.1         2520-3395
FEATURES             Location/Qualifiers
     source          1..3637
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="16"
                     /map="16 11.31 cM"
     gene            1..3637
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /note="TRM2 tRNA methyltransferase 2A"
                     /db_xref="GeneID:15547"
                     /db_xref="MGI:MGI:96270"
     exon            1..369
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     CDS             349..2190
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /EC_number="2.1.1.35"
                     /note="isoform 2 is encoded by transcript variant 2; 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 2"
                     /protein_id="NP_001074468.1"
                     /db_xref="CCDS:CCDS37281.1"
                     /db_xref="GeneID:15547"
                     /db_xref="MGI:MGI:96270"
                     /translation="MSEPAAEVPEPMEDCGQDASAVPSSAAPLCQKEEAGPGPAAGPG
                     TQPGLYSYIRDDLFTSEIFKLELQNVPRHASFSDVRRFLGRFGLQSHKIKLFGQPPCA
                     FVTFRSAAERDKALRVLHGALWKGCPLSVRLARPKADPMARKRRQEGDSEPSVTQIAD
                     VVTPLWTVPYTEQLEQKRLECERVLQKLAKEIGNTNRALLPWLLLQRQQHNKACCPLE
                     GVKPSPQQTEYRNKCEFLVGVGVDGKDNTVGCRLGKYKGGTCAVAAPFDTVHIPEATK
                     QVVKAFQEFIRSTPYSAYDPETYTGHWKQLTVRTSSRGQAMAIAYFHPQKLSSEEVAG
                     LKASLVCHFMEGPGKASGVTSLYFVEEGQRKTPSQEGLPLEHMAGDQCIQEDLLGLTF
                     RISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGI
                     ELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGLVSRLSSHQLVAVLDPPRAGLHS
                     KVILAIRKAENIKRLLYVSCNPRAAMGNFVDLCRAPSNRVKGTPFHPVKAVAVDLFPQ
                     TPHCEMLILFERMQQHPNGIEALEHQEFQTPRNLPDITPQETEISLS"
     exon            370..917
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            918..1026
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1027..1208
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1209..1323
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1324..1439
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1440..1551
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1552..1674
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1675..1750
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1751..1867
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1868..1964
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     exon            1965..3637
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2341..2346
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /note="hexamer: AATAAA"
     polyA_site      2367
                     /gene="Trmt2a"
                     /gene_synonym="Htf9c"
                     /note="major polyA site"
ORIGIN      
        1 gcacttccgc ctgcaggctg agtgcctccg acgctggcgt gagcggctgc tggaaggatc
       61 agtcgggact cggcgcgcgg cggtgacgtc atcggaacca agcccttaga gagaggagac
      121 gcagctagtg tgcgctggcc agccgaaggc aggcgcagcg tgtggccctt ggggacagtg
      181 catccgcaaa cctcagtccc agctctgagc acccgagttt tgagtccctg tgtggagctg
      241 cggtctacct tcacggcggc gtacctcgta tctgcgccct tgttgggtgg gaggccgagc
      301 cggtggtcct cgtgagcacc ctggtccggg caacagacga gccaggagat gagtgagccg
      361 gccgcggaag ttccggagcc catggaggac tgcggccagg atgccagtgc tgtacccagc
      421 tctgcggccc cactatgtca aaaagaggaa gcagggcctg ggccagctgc agggcctgga
      481 acgcagcctg ggctctacag ctacataagg gatgacttgt tcacatcaga aatctttaaa
      541 ctggagctcc aaaatgtacc tcgccacgcc agcttcagtg acgtccggcg ttttctaggc
      601 cgttttggtc tacagtccca caaaatcaaa ctctttggac agccaccatg tgcctttgta
      661 acattccgaa gcgctgctga acgagacaag gccttgcgag tgctgcacgg tgctctctgg
      721 aaaggctgtc cgctcagcgt acgcctggcc cgacccaagg ctgaccccat ggctaggaag
      781 aggcggcaag aaggtgatag tgagccatca gtaacacaaa ttgccgatgt ggtgacccct
      841 ctgtggacag tgccctacac tgagcagctg gagcagaagc gactggaatg tgagcgggtg
      901 ctacagaaac tggccaaaga aattgggaac actaatcgtg ccctgctacc ctggctgctt
      961 ttacagagac aacagcacaa taaagcttgt tgccccctgg agggggtcaa gccatcaccc
     1021 cagcagactg aatatcgtaa taaatgtgaa ttcctggtcg gagttggggt agacggcaag
     1081 gacaacacag ttggctgccg gcttggcaag tacaagggtg gaacatgtgc tgtggcagct
     1141 ccctttgaca ctgtgcacat tccagaggcc actaagcagg tggtgaaggc cttccaggaa
     1201 ttcatccgtt ccacaccata ctcggcatat gaccctgaga catatacagg ccactggaag
     1261 caactgactg ttcgtaccag cagccgaggc caggccatgg ccattgccta cttccatccc
     1321 cagaaactga gctctgagga ggtggcagga ctaaaggcct ccctggtgtg ccacttcatg
     1381 gaggggccag gcaaggccag tggggtgacc tccctctact ttgtggagga gggacagaga
     1441 aagactccca gccaggaagg cctgcccctg gagcatatgg ctggcgacca gtgcattcag
     1501 gaagacctgc tagggctgac cttccgcatc tcccctcatg cattcttcca ggtaaacaca
     1561 cctgcagctg aggtgctcta cacagtaatc caggaatggg cacagctaga tgggggcagt
     1621 acagtgctgg acgtgtgctg tggcactggc accataggcc tggccctggc tccgaaggtg
     1681 aagagagtag tgggaattga actgtgccag gaggctgtgg aggatgcccg gatgaacgcc
     1741 ctcaccaatg agctgagcaa tgttgagttc cactgtggca gggctgagga tctggtgcca
     1801 ggtttggtga gcagactgtc ttcccatcaa cttgtagctg ttctagaccc accacgggct
     1861 ggcctacatt ctaaggtgat tctggccatc cggaaagctg agaacatcaa gcgactcctg
     1921 tatgtttcct gtaaccccag ggcagccatg ggcaactttg tggacctctg cagggcccca
     1981 tctaaccgag taaaaggcac cccattccat ccagtcaagg ctgtggcagt ggacctgttc
     2041 ccacagactc cgcactgtga gatgcttatc ctgtttgaga ggatgcaaca acaccccaat
     2101 ggcatagaag ccctggagca tcaagaattt cagaccccaa gaaatcttcc tgatatcact
     2161 ccacaggaaa cagagatttc cctctcataa gggaagtata ggagcacagg aaagctgggg
     2221 agcgccttac agttccctag taagcagagg gtgactaagc attggtgagg cgtgaggcct
     2281 gcctactaca gttcaatgag tgaacacctg tgtcctaatg atgggacaga cagatttgag
     2341 aataaacaat tgctgatttt actaacattt ctgtggtgaa ccagagcctt aactcattcc
     2401 tacttgccac cttggacaat cctttctgaa aggcaggaag gattctttaa gggtgtcagt
     2461 tttcccagtg ctattactgt gtatttgttt taagacagca tctctatgta gaccagacta
     2521 atctggctta tgactcctga gtgctggcgt taaagtatgt aaactactat gcctgccgaa
     2581 tgccagggct tgcttgaatt tagccccaga gaaccatgtt ttaggaccaa acaccaccca
     2641 ggtattccag gggaacactg aggatagctg aacacaaatc tatgctgagt tcatatggag
     2701 ttaagtgtgt ccactaaggc acttaaaaac acaattgact atagacaacc ttggccagtt
     2761 gaagatccac aaatcagatc cagcactccc atcagaagaa agaaaccagc cattcccttt
     2821 tggacagttt tatgtgttca gaccatcagg gtacacccta cagccttggc caacacacag
     2881 aagcacatca gcacaggctc cccacccttg cagcatgact gtacatataa gacccacctg
     2941 taagagacag ggagggcact ggagaccagg aatgtgtggc agcacctgtt gacagtgcct
     3001 gggtcggtga ggctgcagag ataccaccat taccatatgc tttttcaatg ttaagtatgt
     3061 tttaagggca atggttagtc aaaagactga acacaactga atgggaggca gaaaagaatc
     3121 aagtgtccaa gtctaccaac ttgaattaag ggttcttttt gccaagatta acataaacat
     3181 taactgctgt cacacacatg attaaggagg aggaagatgc tgttgggagg cccacagttg
     3241 ccatcttatc tttctaacag cacatgtcac ccatgtatct tcaggtacat ggttagagac
     3301 actgaggatg tagagtgtag cccctctgaa caggtaatag ggctctgaat acccctctac
     3361 tcaataccca tttacagggg ctatccaatg agcataggta gacaaaaacc tgcaatcagg
     3421 cctggctgca cagagcagct atccttgaga tcaaaaaaca ccataactac ttatcgtgta
     3481 caatgtgcca ggcagctctt ggtcagtgat gggctacatt gaaggccagt tccctattta
     3541 tgcatattca tctgttgaaa tgcatctttc attcttactg taaaagtttc tttccaaatt
     3601 ttaaaacatc ataaaagctt taaaaattga tgaacag
//
