LOCUS       NM_207346               1937 bp    mRNA    linear   PRI 09-OCT-2024
DEFINITION  Homo sapiens tRNA splicing endonuclease subunit 54 (TSEN54), mRNA.
ACCESSION   NM_207346
VERSION     NM_207346.3
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 1937)
  AUTHORS   Fu,B., Zhou,M., Song,G., Zeng,H., Gong,Y., Jiang,Y., Ke,Y.,
            Huang,D., Peng,H. and Li,Q.
  TITLE     Comprehensive analysis reveals TSEN54 as a robust prognosis
            biomarker and promising immune-related therapeutic target for
            hepatocellular carcinoma
  JOURNAL   Aging (Albany NY) 15 (7), 2734-2771 (2023)
   PUBMED   37059591
  REMARK    GeneRIF: Comprehensive analysis reveals TSEN54 as a robust
            prognosis biomarker and promising immune-related therapeutic target
            for hepatocellular carcinoma.
REFERENCE   2  (bases 1 to 1937)
  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   3  (bases 1 to 1937)
  AUTHORS   Sepahvand,A., Razmara,E., Bitarafan,F., Galehdari,M.,
            Tavasoli,A.R., Almadani,N. and Garshasbi,M.
  TITLE     A homozygote variant in the tRNA splicing endonuclease subunit 54
            causes pontocerebellar hypoplasia in a consanguineous Iranian
            family
  JOURNAL   Mol Genet Genomic Med 8 (10), e1413 (2020)
   PUBMED   32697043
  REMARK    GeneRIF: A homozygote variant in the tRNA splicing endonuclease
            subunit 54 causes pontocerebellar hypoplasia in a consanguineous
            Iranian family.
REFERENCE   4  (bases 1 to 1937)
  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   5  (bases 1 to 1937)
  AUTHORS   Maras-Genc,H., Uyur-Yalcin,E., Rosti,R.O., Gleeson,J.G. and Kara,B.
  TITLE     TSEN54 gene-related pontocerebellar hypoplasia type 2 presenting
            with exaggerated startle response: report of two cases in a family
  JOURNAL   Turk J Pediatr 57 (3), 286-289 (2015)
   PUBMED   26701950
  REMARK    GeneRIF: TSEN54 gene-related pontocerebellar hypoplasia type 2
            presented with exaggerated startle response in cousins.
REFERENCE   6  (bases 1 to 1937)
  AUTHORS   Cassandrini,D., Biancheri,R., Tessa,A., Di Rocco,M., Di Capua,M.,
            Bruno,C., Denora,P.S., Sartori,S., Rossi,A., Nozza,P., Emma,F.,
            Mezzano,P., Politi,M.R., Laverda,A.M., Zara,F., Pavone,L.,
            Simonati,A., Leuzzi,V., Santorelli,F.M. and Bertini,E.
  TITLE     Pontocerebellar hypoplasia: clinical, pathologic, and genetic
            studies
  JOURNAL   Neurology 75 (16), 1459-1464 (2010)
   PUBMED   20956791
  REMARK    GeneRIF: We confirm that the common p.A307S mutation in TSEN54 is
            responsible for most of the patients with a PCH2 phenotype.
REFERENCE   7  (bases 1 to 1937)
  AUTHORS   Budde,B.S., Namavar,Y., Barth,P.G., Poll-The,B.T., Nurnberg,G.,
            Becker,C., van Ruissen,F., Weterman,M.A., Fluiter,K., te Beek,E.T.,
            Aronica,E., van der Knaap,M.S., Hohne,W., Toliat,M.R., Crow,Y.J.,
            Steinling,M., Voit,T., Roelenso,F., Brussel,W., Brockmann,K.,
            Kyllerman,M., Boltshauser,E., Hammersen,G., Willemsen,M.,
            Basel-Vanagaite,L., Krageloh-Mann,I., de Vries,L.S., Sztriha,L.,
            Muntoni,F., Ferrie,C.D., Battini,R., Hennekam,R.C., Grillo,E.,
            Beemer,F.A., Stoets,L.M., Wollnik,B., Nurnberg,P. and Baas,F.
  TITLE     tRNA splicing endonuclease mutations cause pontocerebellar
            hypoplasia
  JOURNAL   Nat Genet 40 (9), 1113-1118 (2008)
   PUBMED   18711368
  REMARK    GeneRIF: In two subtypes, PCH2 and PCH4, we identified mutations in
            three of the four different subunits of the tRNA-splicing
            endonuclease complex.
REFERENCE   8  (bases 1 to 1937)
  AUTHORS   Weitzer,S. and Martinez,J.
  TITLE     The human RNA kinase hClp1 is active on 3' transfer RNA exons and
            short interfering RNAs
  JOURNAL   Nature 447 (7141), 222-226 (2007)
   PUBMED   17495927
REFERENCE   9  (bases 1 to 1937)
  AUTHORS   Paushkin,S.V., Patel,M., Furia,B.S., Peltz,S.W. and Trotta,C.R.
  TITLE     Identification of a human endonuclease complex reveals a link
            between tRNA splicing and pre-mRNA 3' end formation
  JOURNAL   Cell 117 (3), 311-321 (2004)
   PUBMED   15109492
REFERENCE   10 (bases 1 to 1937)
  AUTHORS   van Dijk,T. and Baas,F.
  TITLE     TSEN54 Pontocerebellar Hypoplasia
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301773
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BE247638.1, BX424294.2,
            BC053643.1, CV810347.1 and BE251582.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_207346.2.
            
            Summary: This gene encodes a subunit of the tRNA splicing
            endonuclease complex, which catalyzes the removal of introns from
            precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime
            end processing. Mutations in this gene result in pontocerebellar
            hypoplasia type 2.[provided by RefSeq, Oct 2009].
            
            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 :: SRR3476690.1119160.1,
                                           SRR3476690.847105.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA1970526
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000333213.11/ ENSP00000327487.6
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-44                BE247638.1         2-45
            45-89               BX424294.2         24-68
            90-1073             BC053643.1         61-1044
            1074-1198           CV810347.1         408-532
            1199-1342           BC053643.1         1170-1313
            1343-1800           BE251582.1         113-570
            1801-1937           BC053643.1         1772-1908
FEATURES             Location/Qualifiers
     source          1..1937
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17q25.1"
     gene            1..1937
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /note="tRNA splicing endonuclease subunit 54"
                     /db_xref="GeneID:283989"
                     /db_xref="HGNC:HGNC:27561"
                     /db_xref="MIM:608755"
     exon            1..89
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     CDS             34..1614
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /note="tRNA-intron endonuclease Sen54; hsSen54; SEN54
                     homolog; TSEN54 tRNA splicing endonuclease subunit"
                     /codon_start=1
                     /product="tRNA-splicing endonuclease subunit Sen54"
                     /protein_id="NP_997229.2"
                     /db_xref="CCDS:CCDS11724.1"
                     /db_xref="GeneID:283989"
                     /db_xref="HGNC:HGNC:27561"
                     /db_xref="MIM:608755"
                     /translation="MEPEPEPAAVEVPAGRVLSARELFAARSRSQKLPQRSHGPKDFL
                     PDGSAAQAERLRRCREELWQLLAEQRVERLGSLVAAEWRPEEGFVELKSPAGKFWQTM
                     GFSEQGRQRLHPEEALYLLECGSIHLFHQDLPLSIQEAYQLLLTDHTVTFLQYQVFSH
                     LKRLGYVVRRFQPSSVLSPYERQLNLDASVQHLEDGDGKRKRSSSSPRSINKKAKALD
                     NSLQPKSLAASSPPPCSQPSQCPEEKPQESSPMKGPGGPFQLLGSLGPSPGPAREGVG
                     CSWESGRAENGVTGAGKRRWNFEQISFPNMASDSRHTLLRAPAPELLPANVAGRETDA
                     ESWCQKLNQRKEKLSRREREHHAEAAQFQEDVNADPEVQRCSSWREYKELLQRRQVQR
                     SQRRAPHLWGQPVTPLLSPGQASSPAVVLQHISVLQTTHLPDGGARLLEKSGGLEIIF
                     DVYQADAVATFRKNNPGKPYARMCISGFDEPVPDLCSLKRLSYQSGDVPLIFALVDHG
                     DISFYSFRDFTLPQDVGH"
     exon            90..254
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            255..318
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            319..402
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            403..501
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            502..554
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            555..656
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            657..1285
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            1286..1346
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            1347..1463
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     exon            1464..1937
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1917..1922
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /note="hexamer: ATTAAA"
     polyA_site      1937
                     /gene="TSEN54"
                     /gene_synonym="PCH2A; PCH4; PCH5; sen54; SEN54L"
                     /note="major polyA site"
ORIGIN      
        1 gtggcggcgc gcgcagcggc aggcggcggc gggatggagc ccgagcccga gcccgcggcc
       61 gtggaggttc ccgcggggcg cgtgctcagc gcccgggagc tcttcgccgc ccgctcgcgg
      121 tcgcagaagc tgccccagcg ctcgcatggc cccaaggact ttctgcccga cggctcggca
      181 gctcaggccg agcggctgcg ccggtgccgg gaagagctct ggcagctgct ggcagagcag
      241 cgcgtggagc gcctgggcag cttggtggct gccgagtgga ggccagaaga gggcttcgtg
      301 gagttgaagt ctcccgcggg caaattctgg cagaccatgg gcttctcaga gcagggccgg
      361 cagcgccttc acccggaaga ggccttgtat cttctggagt gtggctccat ccacctcttc
      421 caccaagacc tgccactgtc tatccaggaa gcttaccagc tgctgctgac cgaccacact
      481 gtgaccttcc tgcagtacca ggtcttcagc cacctgaaga ggttgggtta tgtggttcga
      541 cgattccaac caagctctgt cctgtccccg tatgagaggc agcttaacct ggatgccagc
      601 gtgcagcact tggaggatgg agatggcaag agaaagagga gcagctccag ccctcggtcc
      661 attaataaga aggccaaggc cctggacaac tccctgcaac ccaagagtct ggcagcctcc
      721 agcccacctc cctgcagcca gcccagccaa tgcccagagg agaaacccca ggagtcaagc
      781 cccatgaagg gcccaggggg cccctttcag cttctggggt ccctgggccc cagccctggc
      841 ccggccaggg agggggtggg gtgcagctgg gagagtggca gagccgagaa cggagtcacg
      901 ggagccggta agcggcgctg gaacttcgag cagatctcct tccccaacat ggcttcagac
      961 agccgccaca cccttctgcg cgccccagcc ccagagctgc tcccggccaa cgtggctggg
     1021 cgggagacag acgctgagtc ctggtgccag aagctgaacc agcgcaagga gaagctctcc
     1081 aggcgggaac gggagcacca cgcggaggcc gcgcagttcc aggaagatgt caacgccgat
     1141 cccgaggtgc agcggtgctc cagctggcgg gagtacaagg agctgctgca gcggcggcag
     1201 gtgcagagga gccagcgccg ggcccctcac ctgtggggcc agcccgtcac cccgctgctg
     1261 agtcctggcc aggccagctc cccagccgtg gtccttcagc atatctctgt gctgcagaca
     1321 acacaccttc ctgatggagg tgcccggctg ttggagaagt ctgggggctt ggaaatcatc
     1381 tttgatgttt accaggccga cgctgtggcc acattccgaa agaataaccc tggcaaaccc
     1441 tatgcccgga tgtgcattag tggatttgat gagcctgtcc cagacctctg cagcctcaag
     1501 cggttgtctt accagagtgg ggatgtccct ctgatctttg ccctggtgga tcatggtgac
     1561 atctccttct acagcttcag ggacttcacg ttgccccagg atgtggggca ctgacctcac
     1621 agctctgcag aggatggagc ttgctccggg ggaccgggac tgtctgttct cagggaccat
     1681 ctcggctgcc tcctgtaccc agactctaac ctgtagcttc agaggccagt ctgggccttg
     1741 gccctgggtg tctgatactc acagagtgaa actgtgaccc tctcccttcc ctgctgcctt
     1801 gcagtgaccc ctctggaact caggactcga ttttaaggac ccaggaggtg gggcagaaga
     1861 gaggactgtg tgcctttaac gagagggtgc ctgcttcgtg ctataaagcc aaagccatta
     1921 aaaatagatt tcttttc
//
