LOCUS       NM_018146               1729 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens mitochondrial rRNA methyltransferase 3 (MRM3),
            transcript variant 1, mRNA; nuclear gene for mitochondrial product.
ACCESSION   NM_018146
VERSION     NM_018146.4
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 1729)
  AUTHORS   Zhou,Y., Liu,Y., Gupta,S., Paramo,M.I., Hou,Y., Mao,C., Luo,Y.,
            Judd,J., Wierbowski,S., Bertolotti,M., Nerkar,M., Jehi,L.,
            Drayman,N., Nicolaescu,V., Gula,H., Tay,S., Randall,G., Wang,P.,
            Lis,J.T., Feschotte,C., Erzurum,S.C., Cheng,F. and Yu,H.
  TITLE     A comprehensive SARS-CoV-2-human protein-protein interactome
            reveals COVID-19 pathobiology and potential host therapeutic
            targets
  JOURNAL   Nat Biotechnol 41 (1), 128-139 (2023)
   PUBMED   36217030
REFERENCE   2  (bases 1 to 1729)
  AUTHORS   Rebelo-Guiomar,P., Pellegrino,S., Dent,K.C., Sas-Chen,A.,
            Miller-Fleming,L., Garone,C., Van Haute,L., Rogan,J.F., Dinan,A.,
            Firth,A.E., Andrews,B., Whitworth,A.J., Schwartz,S., Warren,A.J.
            and Minczuk,M.
  TITLE     A late-stage assembly checkpoint of the human mitochondrial
            ribosome large subunit
  JOURNAL   Nat Commun 13 (1), 929 (2022)
   PUBMED   35177605
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1729)
  AUTHORS   Morgenstern,M., Peikert,C.D., Lubbert,P., Suppanz,I., Klemm,C.,
            Alka,O., Steiert,C., Naumenko,N., Schendzielorz,A., Melchionda,L.,
            Muhlhauser,W.W.D., Knapp,B., Busch,J.D., Stiller,S.B.,
            Dannenmaier,S., Lindau,C., Licheva,M., Eickhorst,C., Galbusera,R.,
            Zerbes,R.M., Ryan,M.T., Kraft,C., Kozjak-Pavlovic,V., Drepper,F.,
            Dennerlein,S., Oeljeklaus,S., Pfanner,N., Wiedemann,N. and
            Warscheid,B.
  TITLE     Quantitative high-confidence human mitochondrial proteome and its
            dynamics in cellular context
  JOURNAL   Cell Metab 33 (12), 2464-2483 (2021)
   PUBMED   34800366
REFERENCE   4  (bases 1 to 1729)
  AUTHORS   Chen,Z., Wang,C., Feng,X., Nie,L., Tang,M., Zhang,H., Xiong,Y.,
            Swisher,S.K., Srivastava,M. and Chen,J.
  TITLE     Interactomes of SARS-CoV-2 and human coronaviruses reveal host
            factors potentially affecting pathogenesis
  JOURNAL   EMBO J 40 (17), e107776 (2021)
   PUBMED   34232536
REFERENCE   5  (bases 1 to 1729)
  AUTHORS   Cai,T., Yu,Z., Wang,Z., Liang,C. and Richard,S.
  TITLE     Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates
            RNA binding, its ability to suppress stress granule formation, and
            viral replication
  JOURNAL   J Biol Chem 297 (1), 100821 (2021)
   PUBMED   34029587
REFERENCE   6  (bases 1 to 1729)
  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   7  (bases 1 to 1729)
  AUTHORS   Lee,K.W. and Bogenhagen,D.F.
  TITLE     Assignment of 2'-O-methyltransferases to modification sites on the
            mammalian mitochondrial large subunit 16 S ribosomal RNA (rRNA)
  JOURNAL   J Biol Chem 289 (36), 24936-24942 (2014)
   PUBMED   25074936
  REMARK    GeneRIF: Data show that 2'-O-methyltransferases MRM1, MRM2, and
            RNMTL1 are responsible for modification of large subunit rRNA at
            residues G1145, U1369, and G1370, respectively.
REFERENCE   8  (bases 1 to 1729)
  AUTHORS   Rorbach,J., Boesch,P., Gammage,P.A., Nicholls,T.J., Pearce,S.F.,
            Patel,D., Hauser,A., Perocchi,F. and Minczuk,M.
  TITLE     MRM2 and MRM3 are involved in biogenesis of the large subunit of
            the mitochondrial ribosome
  JOURNAL   Mol Biol Cell 25 (17), 2542-2555 (2014)
   PUBMED   25009282
  REMARK    GeneRIF: MRM2 and MRM3 are human mitochondrial methyltransferases
            involved in the modification of 16S rRNA and are important factors
            for the biogenesis and function of the large subunit of the
            mitochondrial ribosome.
REFERENCE   9  (bases 1 to 1729)
  AUTHORS   Lee,K.W., Okot-Kotber,C., LaComb,J.F. and Bogenhagen,D.F.
  TITLE     Mitochondrial ribosomal RNA (rRNA) methyltransferase family members
            are positioned to modify nascent rRNA in foci near the
            mitochondrial DNA nucleoid
  JOURNAL   J Biol Chem 288 (43), 31386-31399 (2013)
   PUBMED   24036117
REFERENCE   10 (bases 1 to 1729)
  AUTHORS   Xu,J., De Zhu,J., Ni,M., Wan,F. and Gu,J.R.
  TITLE     The ATF/CREB site is the key element for transcription of the human
            RNA methyltransferase like 1(RNMTL1) gene, a newly discovered
            17p13.3 gene
  JOURNAL   Cell Res 12 (3-4), 177-197 (2002)
   PUBMED   12296377
  REMARK    GeneRIF: The ATF/CREB site is the key element for transcription of
            this protein found on human chromosome 17.
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF177344.2 and AK222900.1.
            
            On Nov 22, 2018 this sequence version replaced NM_018146.3.
            
            Summary: Efficient translation of mitochondrial-derived transcripts
            requires proper assembly of the large subunit of the mitochondrial
            ribosome. Central to the biogenesis of this large subunit is the
            A-loop of mitochondrial 16S rRNA, which is modified by three rRNA
            methyltransferases located near mtDNA nucleoids. The protein
            encoded by this gene methylates G(1370) of 16S rRNA, and this
            modification is necessary for proper ribosomal large subnit
            assembly. Two transcript variants encoding different isoforms have
            been found for this gene. [provided by RefSeq, Dec 2015].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            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 :: AK222900.1, AF177344.2 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            gene product(s) localized to mito. :: reported by MitoCarta
            MANE Ensembl match                 :: ENST00000304478.9/
                                                  ENSP00000306080.4
            RefSeq Select criteria             :: based on conservation,
                                                  expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1721              AF177344.2         81-1801
            1722-1729           AK222900.1         1722-1729
FEATURES             Location/Qualifiers
     source          1..1729
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17p13.3"
     gene            1..1729
                     /gene="MRM3"
                     /gene_synonym="RMTL1; RNMTL1"
                     /note="mitochondrial rRNA methyltransferase 3"
                     /db_xref="GeneID:55178"
                     /db_xref="HGNC:HGNC:18485"
                     /db_xref="MIM:612600"
     exon            1..340
                     /gene="MRM3"
                     /gene_synonym="RMTL1; RNMTL1"
                     /inference="alignment:Splign:2.1.0"
     CDS             27..1289
                     /gene="MRM3"
                     /gene_synonym="RMTL1; RNMTL1"
                     /EC_number="2.1.1.-"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; putative RNA methyltransferase; RNA
                     methyltransferase-like protein 1; 16S rRNA [Gm1370]
                     2'-O-methyltransferase; 16S rRNA
                     (guanosine(1370)-2'-O)-methyltransferase; rRNA
                     methyltransferase 3, mitochondrial; RNA methyltransferase
                     like 1"
                     /codon_start=1
                     /product="rRNA methyltransferase 3, mitochondrial isoform
                     1 precursor"
                     /protein_id="NP_060616.1"
                     /db_xref="CCDS:CCDS10997.1"
                     /db_xref="GeneID:55178"
                     /db_xref="HGNC:HGNC:18485"
                     /db_xref="MIM:612600"
                     /translation="MAALVRPARFVVRPLLQVVQAWDLDARRWVRALRRSPVKVVFPS
                     GEVVEQKRAPGKQPRKAPSEASAQEQREKQPLEESASRAPSTWEESGLRYDKAYPGDR
                     RLSSVMTIVKSRPFREKQGKILLEGRRLISDALKAGAVPKMFFFSRLEYLKELPVDKL
                     KGVSLIKVKFEDIKDWSDLVTPQGIMGIFAKPDHVKMTYPKTQLQHSLPLLLICDNLR
                     DPGNLGTILRSAAGAGCSKVLLTKGCVDAWEPKVLRAGMGAHFRMPIINNLEWETVPN
                     YLPPDTRVYVADNCGLYAQAEMSNKASDHGWVCDQRVMKFHKYEEEEDVETGASQDWL
                     PHVEVQSYDSDWTEAPAAVVIGGETYGVSLESLQLAESTGGKRLLIPVVPGVDSLNSA
                     MAASILLFEGKRQLRGRAEDLSRDRSYH"
     exon            341..585
                     /gene="MRM3"
                     /gene_synonym="RMTL1; RNMTL1"
                     /inference="alignment:Splign:2.1.0"
     exon            586..753
                     /gene="MRM3"
                     /gene_synonym="RMTL1; RNMTL1"
                     /inference="alignment:Splign:2.1.0"
     exon            754..1729
                     /gene="MRM3"
                     /gene_synonym="RMTL1; RNMTL1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1702..1707
                     /regulatory_class="polyA_signal_sequence"
                     /gene="MRM3"
                     /gene_synonym="RMTL1; RNMTL1"
                     /note="hexamer: AATAAA"
     polyA_site      1729
                     /gene="MRM3"
                     /gene_synonym="RMTL1; RNMTL1"
                     /note="major polyA site"
ORIGIN      
        1 gtgacgcagc ccgggtctca gggaacatgg cggcgctggt gagacccgcg aggtttgtcg
       61 tgcgaccgtt gctgcaggtg gtccaggctt gggaccttga cgcgaggcgc tgggtccggg
      121 cgctgcggcg gagcccagtg aaagtggtgt ttccttccgg agaggtggtg gaacagaagc
      181 gcgctcctgg gaagcagccc cgcaaggcac catctgaggc cagtgcccag gagcaacgag
      241 agaaacaacc gctcgaggag tccgcatccc gcgctcccag cacctgggaa gagtctgggc
      301 ttcgctacga taaagcttat cccggggaca ggaggctgag cagtgtaatg acaatagtaa
      361 agtccaggcc atttcgggaa aaacaaggga agatcctgct ggaaggtcgc aggctcattt
      421 cagacgctct caaggctgga gctgtgccaa aaatgttctt ctttagccgt ctagaatacc
      481 taaaggagtt gccagtcgat aagctgaaag gtgtcagcct cattaaggtg aaatttgagg
      541 atatcaagga ttggtccgac ctcgtaacgc cacaaggaat aatggggatt tttgccaagc
      601 ctgaccatgt taagatgaca tatccaaaga ctcagcttca gcattcactg cctttattat
      661 tgatttgtga caatctccgt gaccctggga acctggggac aattctgaga tctgcagctg
      721 gggcaggctg cagcaaagtg ttactcacca aaggctgtgt ggatgcctgg gagcccaaag
      781 tgctccgggc gggtatgggc gcacatttcc ggatgcccat tatcaataat ctggaatggg
      841 aaaccgtgcc caattacctg ccccctgaca ctcgggtcta tgtggctgac aactgtggcc
      901 tttatgccca ggctgagatg tctaataaag ctagtgacca tggctgggtg tgtgatcaac
      961 gagtgatgaa gtttcacaag tatgaggaag aggaagatgt agaaaccgga gccagtcaag
     1021 attggctgcc tcatgttgag gttcagagtt acgactcgga ctggacagag gcgccggcag
     1081 ctgtggtgat tggcggggag acctacggcg tgagcctgga gtccctgcag ctggccgaga
     1141 gcactggtgg caagaggctg ctgatccccg ttgtgcctgg tgtggacagc ctcaactcgg
     1201 ccatggcggc aagcatcctg cttttcgaag ggaaaagaca gctgcggggg agggcggagg
     1261 acttgagcag ggacaggagt taccactgag gacgcagaag tgacttctgc ttgaggacgt
     1321 ctgcagctcc tcctacacca gcacactggt gggaggctgg cggagtcagt gactatggcc
     1381 cccacgttca ggaggaaggt gtgatgccgt catacagtta caggaaaaat aagaacttcc
     1441 tcagaaagaa caggtccgaa ttcttcctgt cgcgtcactg attttgaggt tcttttttct
     1501 cttggtgaca ataggtgacc cacgtggctc tgtgtgtttt taaaaattgt ccaccaagaa
     1561 gcactttgtg cccagaaagt tcctgaagca tcatcctggc agggaggcgc ctgctccacc
     1621 agctggtggg tgtttgtaat cgccaagcac cagctatagg tcacagccac atcactcaca
     1681 gctgatcact ggttggtgga aaataaacta tgagcagcag attacgtta
//
