LOCUS       NM_199044               4347 bp    mRNA    linear   PRI 09-FEB-2025
DEFINITION  Homo sapiens NOP2/Sun RNA methyltransferase 4 (NSUN4), transcript
            variant 1, mRNA.
ACCESSION   NM_199044 XM_371247
VERSION     NM_199044.4
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 4347)
  AUTHORS   Zhao,Z., Zhou,Y., Lv,P., Zhou,T., Liu,H., Xie,Y., Wu,Z., Wang,X.,
            Zhao,H., Zheng,J. and Jiang,X.
  TITLE     NSUN4 mediated RNA 5-methylcytosine promotes the malignant
            progression of glioma through improving the CDC42 mRNA
            stabilization
  JOURNAL   Cancer Lett 597, 217059 (2024)
   PUBMED   38876383
  REMARK    GeneRIF: NSUN4 mediated RNA 5-methylcytosine promotes the malignant
            progression of glioma through improving the CDC42 mRNA
            stabilization.
            Erratum:[Cancer Lett. 2025 Feb 1;610:217351. doi:
            10.1016/j.canlet.2024.217351.. PMID: 39616022]
REFERENCE   2  (bases 1 to 4347)
  AUTHORS   Kim,S., Tan,S., Ku,J., Widowati,T.A., Ku,D., Lee,K., You,K. and
            Kim,Y.
  TITLE     RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for
            degradation and cytosolic release
  JOURNAL   Mol Cell 84 (15), 2935-2948 (2024)
   PUBMED   39019044
  REMARK    Erratum:[Mol Cell. 2025 Feb 4:S1097-2765(25)00079-6. doi:
            10.1016/j.molcel.2025.01.029.. PMID: 39909040]
REFERENCE   3  (bases 1 to 4347)
  AUTHORS   Cui,M., Qu,F., Wang,L., Liu,X., Yu,J., Tang,Z. and Cheng,D.
  TITLE     m5C RNA methyltransferase-related gene NSUN4 stimulates malignant
            progression of hepatocellular carcinoma and can be a prognostic
            marker
  JOURNAL   Cancer Biomark 33 (3), 389-400 (2022)
   PUBMED   34744073
  REMARK    GeneRIF: m5C RNA methyltransferase-related gene NSUN4 stimulates
            malignant progression of hepatocellular carcinoma and can be a
            prognostic marker.
REFERENCE   4  (bases 1 to 4347)
  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   5  (bases 1 to 4347)
  AUTHORS   Coppieters,N., Dieriks,B.V., Lill,C., Faull,R.L., Curtis,M.A. and
            Dragunow,M.
  TITLE     Global changes in DNA methylation and hydroxymethylation in
            Alzheimer's disease human brain
  JOURNAL   Neurobiol Aging 35 (6), 1334-1344 (2014)
   PUBMED   24387984
  REMARK    GeneRIF: It involves in epigenetic changes during the progression
            of Alzheimer disease pathology.
REFERENCE   6  (bases 1 to 4347)
  AUTHORS   Metodiev,M.D., Spahr,H., Loguercio Polosa,P., Meharg,C., Becker,C.,
            Altmueller,J., Habermann,B., Larsson,N.G. and Ruzzenente,B.
  TITLE     NSUN4 is a dual function mitochondrial protein required for both
            methylation of 12S rRNA and coordination of mitoribosomal assembly
  JOURNAL   PLoS Genet 10 (2), e1004110 (2014)
   PUBMED   24516400
  REMARK    Publication Status: Online-Only
REFERENCE   7  (bases 1 to 4347)
  AUTHORS   Yakubovskaya,E., Guja,K.E., Mejia,E., Castano,S., Hambardjieva,E.,
            Choi,W.S. and Garcia-Diaz,M.
  TITLE     Structure of the essential MTERF4:NSUN4 protein complex reveals how
            an MTERF protein collaborates to facilitate rRNA modification
  JOURNAL   Structure 20 (11), 1940-1947 (2012)
   PUBMED   23022348
REFERENCE   8  (bases 1 to 4347)
  AUTHORS   Spahr,H., Habermann,B., Gustafsson,C.M., Larsson,N.G. and
            Hallberg,B.M.
  TITLE     Structure of the human MTERF4-NSUN4 protein complex that regulates
            mitochondrial ribosome biogenesis
  JOURNAL   Proc Natl Acad Sci U S A 109 (38), 15253-15258 (2012)
   PUBMED   22949673
  REMARK    GeneRIF: analysis of the 3D crystal structure of the human
            MTERF4-NSUN4 complex
REFERENCE   9  (bases 1 to 4347)
  AUTHORS   Camara,Y., Asin-Cayuela,J., Park,C.B., Metodiev,M.D., Shi,Y.,
            Ruzzenente,B., Kukat,C., Habermann,B., Wibom,R., Hultenby,K.,
            Franz,T., Erdjument-Bromage,H., Tempst,P., Hallberg,B.M.,
            Gustafsson,C.M. and Larsson,N.G.
  TITLE     MTERF4 regulates translation by targeting the methyltransferase
            NSUN4 to the mammalian mitochondrial ribosome
  JOURNAL   Cell Metab 13 (5), 527-539 (2011)
   PUBMED   21531335
REFERENCE   10 (bases 1 to 4347)
  AUTHORS   Gratacos,M., Costas,J., de Cid,R., Bayes,M., Gonzalez,J.R.,
            Baca-Garcia,E., de Diego,Y., Fernandez-Aranda,F.,
            Fernandez-Piqueras,J., Guitart,M., Martin-Santos,R., Martorell,L.,
            Menchon,J.M., Roca,M., Saiz-Ruiz,J., Sanjuan,J., Torrens,M.,
            Urretavizcaya,M., Valero,J., Vilella,E., Estivill,X. and
            Carracedo,A.
  CONSRTM   Psychiatric Genetics Network Group
  TITLE     Identification of new putative susceptibility genes for several
            psychiatric disorders by association analysis of regulatory and
            non-synonymous SNPs of 306 genes involved in neurotransmission and
            neurodevelopment
  JOURNAL   Am J Med Genet B Neuropsychiatr Genet 150B (6), 808-816 (2009)
   PUBMED   19086053
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL122001.32.
            
            On Sep 28, 2020 this sequence version replaced NM_199044.3.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR14038192.232110.1,
                                           ERR4352441.361195.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000474844.6/ ENSP00000419740.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-113               AL122001.32        83030-83142         c
            114-457             AL122001.32        78805-79148         c
            458-612             AL122001.32        76874-77028         c
            613-773             AL122001.32        70921-71081         c
            774-898             AL122001.32        63121-63245         c
            899-4347            AL122001.32        58931-62379         c
FEATURES             Location/Qualifiers
     source          1..4347
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p33"
     gene            1..4347
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /note="NOP2/Sun RNA methyltransferase 4"
                     /db_xref="GeneID:387338"
                     /db_xref="HGNC:HGNC:31802"
                     /db_xref="MIM:615394"
     exon            1..113
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /inference="alignment:Splign:2.1.0"
     CDS             21..1175
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /note="isoform a is encoded by transcript variant 1;
                     putative methyltransferase NSUN4; NOL1/NOP2/Sun domain
                     family member 4; sperm head and tail associated protein;
                     5-methylcytosine rRNA methyltransferase NSUN4; NOP2/Sun
                     RNA methyltransferase family member 4; NOP2/Sun domain
                     family, member 4; 5-methylcytosine tRNA methyltransferase
                     NSUN4; 5-cytosine tRNA methyltransferase NSUN4; mRNA
                     cytosine C(5)-methyltransferase NSUN4; 5-cytosine rRNA
                     methyltransferase NSUN4"
                     /codon_start=1
                     /product="5-cytosine rRNA methyltransferase NSUN4 isoform
                     a"
                     /protein_id="NP_950245.2"
                     /db_xref="CCDS:CCDS534.1"
                     /db_xref="GeneID:387338"
                     /db_xref="HGNC:HGNC:31802"
                     /db_xref="MIM:615394"
                     /translation="MAALTLRGVRELLKRVDLATVPRRHRYKKKWAATEPKFPAVRLA
                     LQNFDMTYSVQFGDLWPSIRVSLLSEQKYGALVNNFAAWDHVSAKLEQLSAKDFVNEA
                     ISHWELQSEGGQSAAPSPASWACSPNLRCFTFDRGDISRFPPARPGSLGVMEYYLMDA
                     ASLLPVLALGLQPGDIVLDLCAAPGGKTLALLQTGCCRNLAANDLSPSRIARLQKILH
                     SYVPEEIRDGNQVRVTSWDGRKWGELEGDTYDRVLVDVPCTTDRHSLHEEENNIFKRS
                     RKKERQILPVLQVQLLAAGLLATKPGGHVVYSTCSLSHLQNEYVVQGAIELLANQYSI
                     QVQVEDLTHFRRVFMDTFCFFSSCQVGELVIPNLMANFGPMYFCKMRRLT"
     exon            114..457
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /inference="alignment:Splign:2.1.0"
     exon            458..612
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /inference="alignment:Splign:2.1.0"
     exon            613..773
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /inference="alignment:Splign:2.1.0"
     exon            774..898
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /inference="alignment:Splign:2.1.0"
     exon            899..4347
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1500..1505
                     /regulatory_class="polyA_signal_sequence"
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /note="hexamer: AATAAA"
     polyA_site      1520
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /note="major polyA site"
     regulatory      4329..4334
                     /regulatory_class="polyA_signal_sequence"
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
                     /note="hexamer: AATAAA"
     polyA_site      4347
                     /gene="NSUN4"
                     /gene_synonym="SHTAP"
ORIGIN      
        1 accccgtgga gcacgccgat atggctgcgc tgacactgag gggtgtccgg gagctgctga
       61 agcgtgtgga cctcgcgacg gtcccgcgga gacatcgata taagaagaaa tgggctgcca
      121 cagagcccaa attccctgct gttcgactgg ctttgcagaa ttttgacatg acttacagtg
      181 tgcagtttgg agatctttgg ccatcaatcc gtgtcagtct cctctcagag cagaagtatg
      241 gtgcactggt caataacttt gctgcctggg atcatgtaag tgctaagctg gagcagctga
      301 gtgccaagga ttttgtgaat gaagccatct cccactggga actgcagtct gagggtggcc
      361 aatctgcagc cccatcccct gcctcctggg cctgcagtcc gaaccttcga tgcttcactt
      421 ttgacagagg ggatatcagt cgcttccctc ctgccagacc tggcagcctg ggtgtcatgg
      481 agtactacct gatggatgct gcctccttgc tgcctgttct ggccctcggc ctgcagcctg
      541 gggacatcgt gcttgaccta tgtgcagctc ctgggggaaa gacactagcg ttgcttcaga
      601 ctggctgttg ccgcaatctt gctgccaatg atctctcccc gtcccgaata gccagactac
      661 agaagatcct tcacagctat gtgcctgaag agatcaggga tggaaatcaa gttcgagtta
      721 cctcatggga tggcaggaaa tggggagaac tggaggggga cacctatgac cgggtgctgg
      781 tggatgtgcc ctgtaccaca gaccgccact cccttcatga ggaggagaac aacatcttta
      841 agcggtcaag gaagaaggag cgacagatat tgcctgtgct gcaagtgcag cttcttgcgg
      901 ctggactcct tgccaccaaa ccaggaggcc atgttgtcta ttctacctgc tcactctcac
      961 acttacagaa cgagtatgtg gtgcaaggtg ccattgagct cctggccaat caatacagca
     1021 tccaggtaca ggtggaagat ctgactcact tccgaagggt tttcatggac acattttgtt
     1081 tcttctcatc ctgtcaggtt ggggagctgg taataccaaa cctcatggcc aattttggcc
     1141 ccatgtactt ctgcaaaatg cgtaggctga catagtatca cccaatccct gaagcaagaa
     1201 tacaaagggt atactctgtt ggatgcacca gaaactggaa actgggacca gtggcagaga
     1261 tgcactctcg gtcctgtctc catcctgttc gtgtctttct gcagttttcg gcaataagaa
     1321 gtagaagatt tgctgtcctg ctgtccaatt gtggagcatc agcaggtttc caactcactc
     1381 attaacccct accccatctc caggcctgta ctaaagtttg ctgcccgctt aggggcttag
     1441 aaggagaagc cagtgagcag gctcacacta agttgtaaac ataggagaag catttggcca
     1501 ataaagttgt tgaaactcta tagacctggg gctgcagttg gggacttcat gtcagtgcaa
     1561 atgccattag ttccatttgt accagccagt tactgagccc ctgtcaccct tgaagtgagt
     1621 tccacctgac cagtcttgag cagccaacag gctcaattaa gcccgcctgg tttttccata
     1681 tggctcatga tctaatttaa ggaacaagta actaaaaatg ttaagccagt gcaaaataat
     1741 ctgcttacct actcacattg gaaaaaccct ctgagctgaa taattctggc cattcctgct
     1801 gtcaacaata ctgctgccca aatgtggctt aggaggctgc ttctgccaca aaaccgtcat
     1861 actcttgtgc gtgccttgtt ctttgttcat tcatctagca ggtattccca gacctcgtgt
     1921 atgacaggta gctagggagc tcttggagat gtagcagttg ggattgtggg agattactgg
     1981 gcttcctcat cctttagaat ggtaactctc cttttgcttt ctgaacacct aggaatttcc
     2041 tgatgttttg ttttgttgga ttccagactt tttgttgttt ctagtctgca gctgagctct
     2101 ggtgcctgtt ctttggccca ccccctaatc cctaactctt ccctcagcat cacagggctt
     2161 cactgcacac actgtgttca gggcaagatt tcatcattta ctgactgcat actcgatatg
     2221 ttgtttttgt aactttagcc aaaagaaagt aacctttagt ggcagggata taaaaaattg
     2281 ctcagggtca cttgcagata ttttattttt aaactttttt tttttttcct ggaaaacatc
     2341 ctgtgcagaa aagggtatat aattttagaa tacctgaagg cttcttggct tttccacttt
     2401 ccttattcct cctcttcctg ccactctttt tgtcccttct gtctttcctg ctcatcctta
     2461 tttgggtatt agaggtgtca gttgaggagg gactttagct gaggttaagc cttcttttgg
     2521 gatttgcatt gtaattgagg gccctggaag atctctgaga ctcaaaatca ggtgaagcta
     2581 ggaagatgga gctttaagga gcatggctag tgctctgagt aggaccgtaa ccgcctccgt
     2641 gcgtggcata tggtccctgc atgctgttca ctctgtatag tacttagtat tcgctgaggc
     2701 taagaggcct caggtgcctg ggcttctgcc cttggactcc tggatatcca gcctagtgct
     2761 aattgaatgc taagcagtgg taattcaaaa tgagagggtc ccctgcctct agagtcatca
     2821 tctaattggg gacaggcaga cctagataag aaaagcagag aactactttg gaaaacagtt
     2881 tatctgctgt aattgaacat tcagctaccc tataacccag ttaatccaat actggggata
     2941 aatcctagag aaactcatac atgtacacca ggagatgtgt acaagaatat tcatagcaac
     3001 cctattcaca aaagcaaaag cctagaaata acccagatgc ccatgagcaa gagagtggac
     3061 aagtaaactg gaatattcac ataatagaac attatacaat tgtcaaatga actataatga
     3121 tacctaacca tatggatgaa tctgagcaat aaaataatta agtgaaaaaa gtttaatccc
     3181 agaagagtaa atgtagcatg atgccctttc taaatgaaag gttttttctt ttctatggag
     3241 ttattcttta catacaatat agttcataaa ttttaaatat attgtttaat aaattttgat
     3301 aattgtatat aatagtatag tcaccatcaa gatgtagaaa atagaaaata ggctaggcac
     3361 agtggctcac gcctgtaatc tcaacacttt gggaggccaa ggtgggaaga tcacttgatc
     3421 ccaggaattc tagatcagct tggacaatgt agtgagacct ggtctttacc aaaaaaaaaa
     3481 aaaaaaaaat tagctgggtg cgctggcatg tgcctgtggt cccagctact caggaggctg
     3541 aggcaggagg atcacttgag cacaggagtt tgaggctgca gtgagcagcc tgggcaagag
     3601 agtgagactc cgttttgtgc cactgcactc cagccagggt gacagagtga gactctgtct
     3661 caaaaaaaaa aaaaaaaaaa aaggcattgg gatttataat gtgctgttta aagtctgaag
     3721 ctcggccagg tgcggtggct cacgcctgta atcccaaaac tttggaaggc tgaggcaggt
     3781 ggatcacctg aggtcaggag gagttcaaga ccagcctggc caacgtggtg aaaccccatc
     3841 tctataaaag tacaaaaggg catgatggca ggtgcctgta atctcagcta ctcagtaggc
     3901 tggagcggga gaactgcttg aacctgggag gtggaggttt cagtgagcca agatagcgcc
     3961 attgcactcc agcgtgggcg acagcaagag acttcatttc gataaataag taaataaata
     4021 aataaagtct gaagctccac tggtcactcc ttttattgat tatttgcagc tggtctaacc
     4081 agttacgtat gtctggcttg attacatggc cagagcaaca taaaagccct gctgggaact
     4141 tctgatttga gctcttccaa aaccaggatg gatgcctcac atagatcatg atgattcaat
     4201 ccaaaggcac tttgcagtgc agtccacatg tgcataagga ccatggggag cttgtatttg
     4261 ggaattctga gattcctgat gtttacctac ctagtctttc tcttgctgcc ctgtatcctt
     4321 tgcctttaaa taaaaatctt aagtgat
//
