LOCUS       NM_139169               3406 bp    mRNA    linear   PRI 09-FEB-2025
DEFINITION  Homo sapiens TruB pseudouridine synthase family member 1 (TRUB1),
            mRNA.
ACCESSION   NM_139169
VERSION     NM_139169.5
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 3406)
  AUTHORS   Xuan,Y., Wang,L., Zhang,L., Lv,M., Li,F. and Gong,Q.
  TITLE     Structural basis of pri-let-7 recognition by human pseudouridine
            synthase TruB1
  JOURNAL   Biochem Biophys Res Commun 721, 150122 (2024)
   PUBMED   38776834
  REMARK    GeneRIF: Structural basis of pri-let-7 recognition by human
            pseudouridine synthase TruB1.
REFERENCE   2  (bases 1 to 3406)
  AUTHORS   Dai,Q., Zhang,L.S., Sun,H.L., Pajdzik,K., Yang,L., Ye,C., Ju,C.W.,
            Liu,S., Wang,Y., Zheng,Z., Zhang,L., Harada,B.T., Dou,X.,
            Irkliyenko,I., Feng,X., Zhang,W., Pan,T. and He,C.
  TITLE     Quantitative sequencing using BID-seq uncovers abundant
            pseudouridines in mammalian mRNA at base resolution
  JOURNAL   Nat Biotechnol 41 (3), 344-354 (2023)
   PUBMED   36302989
  REMARK    GeneRIF: Quantitative sequencing using BID-seq uncovers abundant
            pseudouridines in mammalian mRNA at base resolution.
REFERENCE   3  (bases 1 to 3406)
  AUTHORS   Jia,Z., Meng,F., Chen,H., Zhu,G., Li,X., He,Y., Zhang,L., He,X.,
            Zhan,H., Chen,M., Ji,Y., Wang,M. and Guan,M.X.
  TITLE     Human TRUB1 is a highly conserved pseudouridine synthase
            responsible for the formation of Psi55 in mitochondrial tRNAAsn,
            tRNAGln, tRNAGlu and tRNAPro
  JOURNAL   Nucleic Acids Res 50 (16), 9368-9381 (2022)
   PUBMED   36018806
  REMARK    GeneRIF: Human TRUB1 is a highly conserved pseudouridine synthase
            responsible for the formation of Psi55 in mitochondrial tRNAAsn,
            tRNAGln, tRNAGlu and tRNAPro.
REFERENCE   4  (bases 1 to 3406)
  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 3406)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   6  (bases 1 to 3406)
  AUTHORS   Carlile,T.M., Martinez,N.M., Schaening,C., Su,A., Bell,T.A.,
            Zinshteyn,B. and Gilbert,W.V.
  TITLE     mRNA structure determines modification by pseudouridine synthase 1
  JOURNAL   Nat Chem Biol 15 (10), 966-974 (2019)
   PUBMED   31477916
REFERENCE   7  (bases 1 to 3406)
  AUTHORS   Safra,M., Nir,R., Farouq,D., Vainberg Slutskin,I. and Schwartz,S.
  TITLE     TRUB1 is the predominant pseudouridine synthase acting on mammalian
            mRNA via a predictable and conserved code
  JOURNAL   Genome Res 27 (3), 393-406 (2017)
   PUBMED   28073919
  REMARK    Erratum:[Genome Res. 2017 Aug;27(8):1460. doi:
            10.1101/gr.225870.117.. PMID: 28765290]
REFERENCE   8  (bases 1 to 3406)
  AUTHORS   Grupe,A., Li,Y., Rowland,C., Nowotny,P., Hinrichs,A.L., Smemo,S.,
            Kauwe,J.S., Maxwell,T.J., Cherny,S., Doil,L., Tacey,K., van
            Luchene,R., Myers,A., Wavrant-De Vrieze,F., Kaleem,M.,
            Hollingworth,P., Jehu,L., Foy,C., Archer,N., Hamilton,G.,
            Holmans,P., Morris,C.M., Catanese,J., Sninsky,J., White,T.J.,
            Powell,J., Hardy,J., O'Donovan,M., Lovestone,S., Jones,L.,
            Morris,J.C., Thal,L., Owen,M., Williams,J. and Goate,A.
  TITLE     A scan of chromosome 10 identifies a novel locus showing strong
            association with late-onset Alzheimer disease
  JOURNAL   Am J Hum Genet 78 (1), 78-88 (2006)
   PUBMED   16385451
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   9  (bases 1 to 3406)
  AUTHORS   Deloukas,P., Earthrowl,M.E., Grafham,D.V., Rubenfield,M.,
            French,L., Steward,C.A., Sims,S.K., Jones,M.C., Searle,S.,
            Scott,C., Howe,K., Hunt,S.E., Andrews,T.D., Gilbert,J.G.,
            Swarbreck,D., Ashurst,J.L., Taylor,A., Battles,J., Bird,C.P.,
            Ainscough,R., Almeida,J.P., Ashwell,R.I., Ambrose,K.D.,
            Babbage,A.K., Bagguley,C.L., Bailey,J., Banerjee,R., Bates,K.,
            Beasley,H., Bray-Allen,S., Brown,A.J., Brown,J.Y., Burford,D.C.,
            Burrill,W., Burton,J., Cahill,P., Camire,D., Carter,N.P.,
            Chapman,J.C., Clark,S.Y., Clarke,G., Clee,C.M., Clegg,S., Corby,N.,
            Coulson,A., Dhami,P., Dutta,I., Dunn,M., Faulkner,L., Frankish,A.,
            Frankland,J.A., Garner,P., Garnett,J., Gribble,S., Griffiths,C.,
            Grocock,R., Gustafson,E., Hammond,S., Harley,J.L., Hart,E.,
            Heath,P.D., Ho,T.P., Hopkins,B., Horne,J., Howden,P.J., Huckle,E.,
            Hynds,C., Johnson,C., Johnson,D., Kana,A., Kay,M., Kimberley,A.M.,
            Kershaw,J.K., Kokkinaki,M., Laird,G.K., Lawlor,S., Lee,H.M.,
            Leongamornlert,D.A., Laird,G., Lloyd,C., Lloyd,D.M., Loveland,J.,
            Lovell,J., McLaren,S., McLay,K.E., McMurray,A.,
            Mashreghi-Mohammadi,M., Matthews,L., Milne,S., Nickerson,T.,
            Nguyen,M., Overton-Larty,E., Palmer,S.A., Pearce,A.V., Peck,A.I.,
            Pelan,S., Phillimore,B., Porter,K., Rice,C.M., Rogosin,A.,
            Ross,M.T., Sarafidou,T., Sehra,H.K., Shownkeen,R., Skuce,C.D.,
            Smith,M., Standring,L., Sycamore,N., Tester,J., Thorpe,A.,
            Torcasso,W., Tracey,A., Tromans,A., Tsolas,J., Wall,M., Walsh,J.,
            Wang,H., Weinstock,K., West,A.P., Willey,D.L., Whitehead,S.L.,
            Wilming,L., Wray,P.W., Young,L., Chen,Y., Lovering,R.C.,
            Moschonas,N.K., Siebert,R., Fechtel,K., Bentley,D., Durbin,R.,
            Hubbard,T., Doucette-Stamm,L., Beck,S., Smith,D.R. and Rogers,J.
  TITLE     The DNA sequence and comparative analysis of human chromosome 10
  JOURNAL   Nature 429 (6990), 375-381 (2004)
   PUBMED   15164054
REFERENCE   10 (bases 1 to 3406)
  AUTHORS   Zucchini,C., Strippoli,P., Biolchi,A., Solmi,R., Lenzi,L.,
            D'Addabbo,P., Carinci,P. and Valvassori,L.
  TITLE     The human TruB family of pseudouridine synthase genes, including
            the Dyskeratosis Congenita 1 gene and the novel member TRUB1
  JOURNAL   Int J Mol Med 11 (6), 697-704 (2003)
   PUBMED   12736709
  REMARK    GeneRIF: TRUB1 gene encodes a 349-amino acid product, with a
            VFAVHKPKGPTSA box in positions 71-83 corresponding to motif I of
            the TruB family
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BC030601.2 and AL355340.17.
            
            On Nov 23, 2018 this sequence version replaced NM_139169.4.
            
            Summary: Pseudouridine is an abundant component of rRNAs and tRNAs
            and is enzymatically generated by isomerization of uridine by
            pseudouridine synthase (Zucchini et al., 2003 [PubMed
            12736709]).[supplied by OMIM, Mar 2008].
            
            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 :: BX648709.1, BC030601.2 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000298746.5/ ENSP00000298746.3
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1216              BC030601.2         3-1218
            1217-3406           AL355340.17        61393-63582
FEATURES             Location/Qualifiers
     source          1..3406
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10q25.3"
     gene            1..3406
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /note="TruB pseudouridine synthase family member 1"
                     /db_xref="GeneID:142940"
                     /db_xref="HGNC:HGNC:16060"
                     /db_xref="MIM:610726"
     exon            1..345
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /inference="alignment:Splign:2.1.0"
     CDS             60..1109
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /EC_number="5.4.99.25"
                     /note="probable tRNA pseudouridine synthase 1; TruB
                     pseudouridine (psi) synthase homolog 1; psi55 synthase
                     TRUB1; TruB pseudouridine (psi) synthase family member 1;
                     tRNA pseudouridine 55 synthase TRUB1; truB pseudouridine
                     synthase homolog 1"
                     /codon_start=1
                     /product="pseudouridylate synthase TRUB1"
                     /protein_id="NP_631908.1"
                     /db_xref="CCDS:CCDS7591.1"
                     /db_xref="GeneID:142940"
                     /db_xref="HGNC:HGNC:16060"
                     /db_xref="MIM:610726"
                     /translation="MAASEAAVVSSPSLKTDTSPVLETAGTVAAMAATPSARAAAAVV
                     AAAARTGSEARVSKAALATKLLSLSGVFAVHKPKGPTSAELLNRLKEKLLAEAGMPSP
                     EWTKRKKQTLKIGHGGTLDSAARGVLVVGIGSGTKMLTSMLSGSKRYTAIGELGKATD
                     TLDSTGRVTEEKPYDKITQEDIEGILQKFTGNIMQVPPLYSALKKDGQRLSTLMKRGE
                     VVEAKPARPVTVYSISLQKFQPPFFTLDVECGGGFYIRSLVSDIGKELSSCANVLELT
                     RTKQGPFTLEEHALPEDKWTIDDIAQSLEHCSSLFPAELALKKSKPESNEQVLSCEYI
                     TLNEPKREDDVIKTC"
     exon            346..444
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /inference="alignment:Splign:2.1.0"
     exon            445..500
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /inference="alignment:Splign:2.1.0"
     exon            501..582
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /inference="alignment:Splign:2.1.0"
     exon            583..655
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /inference="alignment:Splign:2.1.0"
     exon            656..795
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /inference="alignment:Splign:2.1.0"
     exon            796..852
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /inference="alignment:Splign:2.1.0"
     exon            853..3406
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3382..3387
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /note="hexamer: AATAAA"
     polyA_site      3406
                     /gene="TRUB1"
                     /gene_synonym="PUS4"
                     /note="major polyA site"
ORIGIN      
        1 actcttgttg catcatcagc gtgcacctcc acgatgaaac aggtctgggc tacaaaagta
       61 tggccgcttc tgaggcggcg gtggtgtctt cgccgtcttt gaaaacagac acatcccctg
      121 tccttgaaac tgcaggaacg gtcgcagcaa tggctgcgac cccgtcagca agggctgcag
      181 ccgcggtggt tgcggccgcg gccaggaccg gatccgaagc cagggtctcc aaggccgctt
      241 tggctaccaa gctgctgtcc ttgagcggcg tgttcgccgt gcacaagccc aaagggccca
      301 cttcagccga gctgctgaat cggttgaagg agaagctgct ggcagaagct ggaatgcctt
      361 ctccagaatg gaccaagagg aaaaagcaga ctttgaaaat tgggcatgga gggactctag
      421 acagcgcagc ccgaggagtt ctggttgttg gaattggaag cggaacaaaa atgttgacca
      481 gtatgttgtc agggtccaag agatatactg ccattggaga actggggaaa gctactgata
      541 cactagattc tacggggagg gtaacagaag aaaaacctta cgataaaata acacaagaag
      601 atattgaagg cattctacag aaatttactg gaaatataat gcaagtgccc cccctctatt
      661 ctgcattaaa gaaagatgga caaagacttt cgactttgat gaagagaggt gaagtcgtag
      721 aagcaaaacc tgccaggcca gtgactgtat acagtatctc ccttcaaaaa ttccagccac
      781 catttttcac attagatgtt gaatgtggag gaggttttta tatcagaagc ttggtcagtg
      841 acattggaaa agaactatct tcctgtgcca atgtgctaga gctgacccga accaaacagg
      901 gaccatttac gctagaagaa catgcccttc ctgaagacaa atggacaatt gatgacattg
      961 cacagtctct tgagcattgc tcatctcttt tcccagcaga gttggcactt aaaaaatcaa
     1021 aacctgagtc taatgaacag gttttgagct gtgaatatat aactctaaat gagccaaaga
     1081 gagaagatga tgtaattaag acgtgttgag attggcctgg gaatatcatc attttctagt
     1141 tgacatttga atcctgtgtg cagatgcaga atgacaagct gcattcaaaa gacaaacaat
     1201 atgtcttttt tttttttgca tgaagaaaaa tgtctatcat ttacagtttc aatagcacat
     1261 aatttatttt ctatgcatta taaatggcct tgcagttggc tcagttgttt gttgtgttgt
     1321 gaaatgtttt aggatttttt gtattgtgaa aatatgaata tgattggatt cagaaaaatt
     1381 aactttctga atttgatctg tcttcagtct tgtgaaaaag ttgaacaaat ttcctaatca
     1441 aagaaaaaag tatgagctcc atgtttcttt agtttcacaa aaatgaccat aatttagtgt
     1501 tatttttact ttatttaggc ttcctggtgg cttcatttta ttgaaattct ttaaattgtt
     1561 taaagtggcc attattgatc tctttcttct gttttggaga gtttattatt aaaaacattt
     1621 ctttgataaa atggccatca tctagtaata cctgtgtttg tttagatctt ggaaatgaat
     1681 aagctttgat aatatttgta aatgaaccaa attattactg ctaccactaa caggttgtaa
     1741 atagaagact aatacttaat taaagtcacc ttcctaccat tagagcagaa gacagctcct
     1801 atagttttgt attttggcag ctatgagata ttttcatggt aatgtcaaca tggtcaagca
     1861 ctttgtacca agttattaag taacataatt tttaaaattt aaagaatgtg tcttcaacta
     1921 aaaactttat tctttagcat ttatttatat ttctctgtag ggtgttccct gtgacattgt
     1981 ctctttagtt tgctctttca agagatactt acagatgttg agatggctgc cctgcatttc
     2041 cagctaatct cttctgctct aaatatttaa aaacagttct tctcaaacat tttcattcag
     2101 atagctttct gaaagttccc tatccctctt taccataatt ttttaaatgt agccacattg
     2161 taatagtaaa cttcatatat aatgagtgct tcatattttt gttatgggaa agcaatatat
     2221 tatgcagcca gtctgtagaa acattcagat ccctcttcct ttactcaaat acagtttcaa
     2281 aaggaagact catgagaaat ttcataaaat acaagttttt agatgtttat gctttgcctt
     2341 tctttttaaa ggtgttttcc tgctttgtag tctctaactc tgaaatttaa aatatgtaaa
     2401 ctaaagtggt tttatttgtg cttaacccaa tttaaactca atgtaaaatg ttatatatgc
     2461 atcagtacag cattttcaac atattggcaa catattttaa atgaaaacac taaaacaatt
     2521 cttagtatga gacaaaactg taaggaaaaa gagtgttaat accatgatgc attaacataa
     2581 aatatcaaac acacaaagtc ataaaatgaa aatttacagt tttacctgtt catatctagt
     2641 gccccacagt gtgtgtcaac caaaggtggc agtggctaca tctgcctgtt ggactggtac
     2701 aggttacaat atgtcctctt ccattgcaaa ttaaagtcca aatagagaaa tacttaggtt
     2761 ttagaacaca tcagaggtat ttctgctgta tttttcacct taaaaattga cacagagttt
     2821 actaatagag gagtagagat tgttgaccat ttttaaaaaa cgatagccac tctttttctt
     2881 ttatgtttaa aactgaagtt ttgccaaatg ggaaaattac tgttacctct accatcttaa
     2941 tgtagtaact ttagaattta aatttttata ttactatttt cctttttgtt gttcacatag
     3001 tcttaaggca cctatacttt taaattgact ttttcatttg atattatcta tatgtatgta
     3061 gttgtgataa tgattatttt aattatatta ctttatactc ttaatttatt tagagtattt
     3121 ctctattgct gaatacttaa gtagttttaa attttattat gataaattcc tgggaggggg
     3181 attatttagt gaaataatat gaagaacttt atgacttatg tttgccttat tgcattccca
     3241 aagagttgta acattttaca gtgttaccat ttgagtaggg gttttatatg ttgttgctaa
     3301 tttagtaaac ataggagaga aatcaaagtt tttctgattt gcttttatgt gatttatctg
     3361 tatactttgt tcatttatat aaataaatgt cttaatggtt tctata
//
