LOCUS       NM_182916               2252 bp    mRNA    linear   PRI 06-OCT-2024
DEFINITION  Homo sapiens tRNA nucleotidyl transferase 1 (TRNT1), transcript
            variant 1, mRNA; nuclear gene for mitochondrial product.
ACCESSION   NM_182916
VERSION     NM_182916.3
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 2252)
  AUTHORS   Fatica,T., Naas,T., Liwak,U., Slaa,H., Souaid,M., Frangione,B.,
            Kattini,R., Gaudreau-Lapierre,A., Trinkle-Mulcahy,L.,
            Chakraborty,P. and Holcik,M.
  TITLE     TRNT-1 Deficiency Is Associated with Loss of tRNA Integrity and
            Imbalance of Distinct Proteins
  JOURNAL   Genes (Basel) 14 (5), 1043 (2023)
   PUBMED   37239403
  REMARK    GeneRIF: TRNT-1 Deficiency Is Associated with Loss of tRNA
            Integrity and Imbalance of Distinct Proteins.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2252)
  AUTHORS   Seki,M., Komuro,A., Ishikawa,T., Takahashi,M. and Nashimoto,M.
  TITLE     Genes for tRNA recycling are upregulated in response to infection
            with Theiler's mouse encephalitis virus
  JOURNAL   Biochem Biophys Res Commun 587, 63-68 (2022)
   PUBMED   34864548
  REMARK    GeneRIF: Genes for tRNA recycling are upregulated in response to
            infection with Theiler's mouse encephalitis virus.
REFERENCE   3  (bases 1 to 2252)
  AUTHORS   Odom,J., Amin,H., Gijavanekar,C., Elsea,S.H., Kralik,S., Chinen,J.,
            Lin,Y., Yates,A.M.M., Mizerik,E., Potocki,L. and Scaglia,F.
  TITLE     A phenotypic expansion of TRNT1 associated sideroblastic anemia
            with immunodeficiency, fevers, and developmental delay
  JOURNAL   Am J Med Genet A 188 (1), 259-268 (2022)
   PUBMED   34510712
  REMARK    GeneRIF: A phenotypic expansion of TRNT1 associated sideroblastic
            anemia with immunodeficiency, fevers, and developmental delay.
            Review article
REFERENCE   4  (bases 1 to 2252)
  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 2252)
  AUTHORS   Wang,J., Deng,Q., He,X., Chen,D., Hang,S., Gao,Y. and Chen,Y.
  TITLE     Two cases of sideroblastic anemia with B-cell immunodeficiency,
            periodic fevers, and developmental delay (SIFD) syndrome in Chinese
            Han children caused by novel compound heterozygous variants of the
            TRNT1 gene
  JOURNAL   Clin Chim Acta 521, 244-250 (2021)
   PUBMED   34310935
  REMARK    GeneRIF: Two cases of sideroblastic anemia with B-cell
            immunodeficiency, periodic fevers, and developmental delay (SIFD)
            syndrome in Chinese Han children caused by novel compound
            heterozygous variants of the TRNT1 gene.
REFERENCE   6  (bases 1 to 2252)
  AUTHORS   Augustin,M.A., Reichert,A.S., Betat,H., Huber,R., Morl,M. and
            Steegborn,C.
  TITLE     Crystal structure of the human CCA-adding enzyme: insights into
            template-independent polymerization
  JOURNAL   J Mol Biol 328 (5), 985-994 (2003)
   PUBMED   12729736
  REMARK    GeneRIF: The crystal structure reveals a four domain architecture
            with a cluster of conserved residues forming a positively charged
            cleft between the first two domains.
REFERENCE   7  (bases 1 to 2252)
  AUTHORS   Nagaike,T., Suzuki,T., Tomari,Y., Takemoto-Hori,C., Negayama,F.,
            Watanabe,K. and Ueda,T.
  TITLE     Identification and characterization of mammalian mitochondrial tRNA
            nucleotidyltransferases
  JOURNAL   J Biol Chem 276 (43), 40041-40049 (2001)
   PUBMED   11504732
REFERENCE   8  (bases 1 to 2252)
  AUTHORS   Reichert,A.S., Thurlow,D.L. and Morl,M.
  TITLE     A eubacterial origin for the human tRNA nucleotidyltransferase?
  JOURNAL   Biol Chem 382 (10), 1431-1438 (2001)
   PUBMED   11727826
  REMARK    GeneRIF: human gene transcript CGI-47 (#AF151805) was cloned and
            encodes a bona fide CCA-adding enzyme and not a poly(A) polymerase.
REFERENCE   9  (bases 1 to 2252)
  AUTHORS   Simpson,J.C., Wellenreuther,R., Poustka,A., Pepperkok,R. and
            Wiemann,S.
  TITLE     Systematic subcellular localization of novel proteins identified by
            large-scale cDNA sequencing
  JOURNAL   EMBO Rep 1 (3), 287-292 (2000)
   PUBMED   11256614
REFERENCE   10 (bases 1 to 2252)
  AUTHORS   Fahim,A.T., Daiger,S.P. and Weleber,R.G.
  TITLE     Nonsyndromic Retinitis Pigmentosa Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301590
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB032432.1, AB063105.1,
            AC024060.6, DA884423.1, AL834397.1, BQ722111.1 and DB525237.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 19, 2018 this sequence version replaced NM_182916.2.
            
            Summary: The protein encoded by this gene is a CCA-adding enzyme
            which belongs to the tRNA nucleotidyltransferase/poly(A) polymerase
            family. This essential enzyme functions by catalyzing the addition
            of the conserved nucleotide triplet CCA to the 3' terminus of tRNA
            molecules. Mutations in this gene result in sideroblastic anemia
            with B-cell immunodeficiency, periodic fevers, and developmental
            delay. Alternative splicing results in multiple transcript
            variants. [provided by RefSeq, Dec 2014].
            
            Transcript Variant: This variant (1) 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 :: SRR1803616.52945.1,
                                           SRR1803617.278944.1 [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                 :: ENST00000251607.11/
                                                  ENSP00000251607.6
            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
            1-33                DB032432.1         25-57
            34-145              AB063105.1         1-112
            146-146             AC024060.6         128740-128740       c
            147-1025            AB063105.1         114-992
            1026-1408           DA884423.1         196-578
            1409-1995           AL834397.1         1337-1923
            1996-1998           BQ722111.1         849-851
            1999-2249           DB525237.1         186-436
            2250-2252           AL834397.1         2197-2199
FEATURES             Location/Qualifiers
     source          1..2252
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3p26.2"
     gene            1..2252
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /note="tRNA nucleotidyl transferase 1"
                     /db_xref="GeneID:51095"
                     /db_xref="HGNC:HGNC:17341"
                     /db_xref="MIM:612907"
     exon            1..51
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /inference="alignment:Splign:2.1.0"
     exon            52..226
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /inference="alignment:Splign:2.1.0"
     CDS             79..1383
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /EC_number="2.7.7.72"
                     /note="isoform 1 is encoded by transcript variant 1;
                     mitochondrial CCA-adding tRNA-nucleotidyltransferase; tRNA
                     nucleotidyl transferase, CCA-adding, 1;
                     tRNA-nucleotidyltransferase 1, mitochondrial; CCA tRNA
                     nucleotidyltransferase 1, mitochondrial; mt CCA-adding
                     enzyme; mt tRNA CCA-diphosphorylase; mt tRNA
                     adenylyltransferase; mt tRNA CCA-pyrophosphorylase; tRNA
                     CCA nucleotidyl transferase 1; ATP(CTP):tRNA
                     nucleotidyltransferase"
                     /codon_start=1
                     /product="CCA tRNA nucleotidyltransferase 1, mitochondrial
                     isoform 1"
                     /protein_id="NP_886552.3"
                     /db_xref="CCDS:CCDS2561.2"
                     /db_xref="GeneID:51095"
                     /db_xref="HGNC:HGNC:17341"
                     /db_xref="MIM:612907"
                     /translation="MLRCLYHWHRPVLNRRWSRLCLPKQYLFTMKLQSPEFQSLFTEG
                     LKSLTELFVKENHELRIAGGAVRDLLNGVKPQDIDFATTATPTQMKEMFQSAGIRMIN
                     NRGEKHGTITARLHEENFEITTLRIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFL
                     GFDGTLFDYFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVDKPGDHDPE
                     TLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLE
                     EFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLI
                     KATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHD
                     IRKVGISSGKEIGALLQQLREQWKKSGYQMEKDELLSYIKKT"
     exon            227..420
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /inference="alignment:Splign:2.1.0"
     exon            421..559
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /inference="alignment:Splign:2.1.0"
     exon            560..686
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /inference="alignment:Splign:2.1.0"
     exon            687..880
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /inference="alignment:Splign:2.1.0"
     exon            881..1134
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /inference="alignment:Splign:2.1.0"
     exon            1135..2252
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1816..1821
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /note="hexamer: AATAAA"
     polyA_site      1840
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /note="major polyA site"
     regulatory      2058..2063
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /note="hexamer: AACAAA"
     polyA_site      2083
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /note="major polyA site"
     regulatory      2166..2171
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /note="hexamer: ATTAAA"
     regulatory      2186..2191
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /note="hexamer: ATTATA"
     polyA_site      2191
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
     polyA_site      2202
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
     regulatory      2233..2238
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
                     /note="hexamer: AATAAA"
     polyA_site      2252
                     /gene="TRNT1"
                     /gene_synonym="CCA1; CGI-47; MtCCA; RPEM; SIFD"
ORIGIN      
        1 agcccggaag tgcgcgtggc ggcggtggcg gctgcggcaa cagcggggcc gatgtgtagt
       61 tggtgactgc ctctccagat gctgaggtgc ctgtatcatt ggcacaggcc agtgctgaac
      121 cgtaggtgga gtaggctgtg ccttccgaag cagtatctat tcacaatgaa gttgcagtct
      181 cccgaattcc agtcactttt cacagaagga ctgaagagtc tgacagaatt atttgtcaaa
      241 gagaatcacg aattaagaat agcaggagga gcagtgaggg atttattaaa tggagtaaag
      301 cctcaggata tagattttgc caccactgct acccctactc aaatgaagga gatgtttcag
      361 tcggctggga ttcggatgat aaacaacaga ggagaaaagc acggaacaat tactgccagg
      421 cttcatgaag aaaattttga gattactaca ctacggattg atgtcaccac tgatggaaga
      481 catgctgagg tagaatttac aactgactgg cagaaagatg cggaacgcag agatctcact
      541 ataaattcta tgtttttagg ttttgatggc actttatttg actactttaa tggttatgaa
      601 gatttaaaaa ataagaaagt tagatttgtt ggacatgcta aacagagaat acaagaggat
      661 tatcttagaa ttttaagata cttcaggttt tatgggagaa ttgtagacaa acctggtgac
      721 catgatcctg agactttgga agcaattgca gaaaatgcaa aaggcttggc tggaatatca
      781 ggagaaagga tttgggtgga actgaaaaaa attcttgttg gtaaccatgt aaatcatttg
      841 attcacctta tctatgatct tgatgtggct ccttatatag gtttacctgc taatgcaagt
      901 ttagaagaat ttgacaaagt cagtaaaaat gttgatggtt tttcaccaaa gccagtgact
      961 cttttggcct cattattcaa agtacaagat gatgtcacaa aattggattt gaggttgaag
     1021 atcgcaaaag aggagaaaaa ccttggctta tttatagtta aaaataggaa agatttaatt
     1081 aaagcaacag atagttcaga cccattgaaa ccctatcaag acttcattat agattctagg
     1141 gaacctgatg caactactcg tgtatgtgaa ctactgaagt accaaggaga gcactgtctc
     1201 ctaaaggaaa tgcagcagtg gtccattcct ccatttcctg taagtggcca tgacatcaga
     1261 aaagtgggca tttcttcagg aaaagaaatt ggggctctat tacaacagtt gcgagaacag
     1321 tggaaaaaaa gtggttacca aatggaaaaa gatgaacttc tgagttacat aaagaagacc
     1381 taaaactgat ggctactaaa aagcagagca tttctggtaa gactaaattt tctcccctcc
     1441 ctcttaatga ggttttagag actacaccag aataaaagac agtttagggg acctctgtag
     1501 aacaacaagg gtcttatttt gtgaattata tatttcaaga actaaacaga gatccacctt
     1561 tctggatctg atttatatca ctgaaatgta cagttctttt ggaatagttt cacctgagaa
     1621 aacatagttg gctattatct atcttaacct gttcaggctt ttaaaaaaaa ctgtttttgc
     1681 atagggtagt actaagatct taaaaagtgg taactgtctt gaagaaaaaa cgtttattgt
     1741 ttgtttgcaa ttgaaataac agggttacct taacaatgac tgtctatgat gtgtcagttc
     1801 ttatctgaat tccaaaataa acctgtgctt aaaaaagaaa taattgacca agtaagtttg
     1861 cataaaatgt gaatactaaa tgtgtcccca gttgctggca ttcatatgta caggatttgt
     1921 tctagcaagc tatgcttcag tatgtggttg atatttttct gtcacaatga tttctttatg
     1981 catgcagagc ctggggaagt catgggatta acttgagggt cactattgag cctattaatt
     2041 aattattgtt ttaataaaac aaacattggt attggaagat aaatatgttt atgtggtatc
     2101 tgacaatgtg tattaggtgt catatacaat ggtaatatgc ctgtctttaa agtgttattt
     2161 tattaattaa aaggatatgg ctattattat atattctcta aagatttgag tcctaaatgc
     2221 tttcatcagg taaataaaat gtataataca aa
//
