LOCUS       NM_025265               2753 bp    mRNA    linear   PRI 10-OCT-2024
DEFINITION  Homo sapiens tRNA splicing endonuclease subunit 2 (TSEN2),
            transcript variant 1, mRNA.
ACCESSION   NM_025265
VERSION     NM_025265.4
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 2753)
  AUTHORS   Canpolat,N., Liu,D., Atayar,E., Saygili,S., Kara,N.S.,
            Westfall,T.A., Ding,Q., Brown,B.J., Braun,T.A., Slusarski,D., Karli
            Oguz,K., Ozluk,Y., Tuysuz,B., Tastemel Ozturk,T., Sever,L.,
            Sezerman,O.U., Topaloglu,R., Caliskan,S., Attanasio,M. and
            Ozaltin,F.
  TITLE     A splice site mutation in the TSEN2 causes a new syndrome with
            craniofacial and central nervous system malformations, and atypical
            hemolytic uremic syndrome
  JOURNAL   Clin Genet 101 (3), 346-358 (2022)
   PUBMED   34964109
  REMARK    GeneRIF: A splice site mutation in the TSEN2 causes a new syndrome
            with craniofacial and central nervous system malformations, and
            atypical hemolytic uremic syndrome.
REFERENCE   2  (bases 1 to 2753)
  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 2753)
  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   4  (bases 1 to 2753)
  AUTHORS   Tao,S., Wang,Z., Feng,J., Hsu,F.C., Jin,G., Kim,S.T., Zhang,Z.,
            Gronberg,H., Zheng,L.S., Isaacs,W.B., Xu,J. and Sun,J.
  TITLE     A genome-wide search for loci interacting with known prostate
            cancer risk-associated genetic variants
  JOURNAL   Carcinogenesis 33 (3), 598-603 (2012)
   PUBMED   22219177
REFERENCE   5  (bases 1 to 2753)
  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   6  (bases 1 to 2753)
  AUTHORS   Ballif,B.A., Villen,J., Beausoleil,S.A., Schwartz,D. and Gygi,S.P.
  TITLE     Phosphoproteomic analysis of the developing mouse brain
  JOURNAL   Mol Cell Proteomics 3 (11), 1093-1101 (2004)
   PUBMED   15345747
REFERENCE   7  (bases 1 to 2753)
  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   8  (bases 1 to 2753)
  AUTHORS   Nakayama,M., Kikuno,R. and Ohara,O.
  TITLE     Protein-protein interactions between large proteins: two-hybrid
            screening using a functionally classified library composed of long
            cDNAs
  JOURNAL   Genome Res 12 (11), 1773-1784 (2002)
   PUBMED   12421765
REFERENCE   9  (bases 1 to 2753)
  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 AC090947.2, BC019582.1,
            BM671402.1 and AC018500.4.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_025265.3.
            
            Summary: This gene encodes one of the subunits of the tRNA splicing
            endonuclease. This endonuclease catalyzes the first step in RNA
            splicing which is the removal of introns. Mutations in this gene
            have been associated with pontocerebellar hypoplasia type 2. A
            pseudogene has been identified on chromosome 4. Multiple transcript
            variants encoding different isoforms have been found for this
            gene.[provided by RefSeq, Feb 2009].
            
            Transcript Variant: This variant (1) represents the longer
            transcript. Variants 1, 2 and 6 encode the same isoform (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660803.134131.1,
                                           SRR1660809.209832.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968189
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000284995.11/ ENSP00000284995.6
            RefSeq Select criteria :: based on expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-49                AC090947.2         12258-12306         c
            50-2003             BC019582.1         1-1954
            2004-2416           BM671402.1         18-430              c
            2417-2753           AC018500.4         75085-75421
FEATURES             Location/Qualifiers
     source          1..2753
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3p25.2"
     gene            1..2753
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /note="tRNA splicing endonuclease subunit 2"
                     /db_xref="GeneID:80746"
                     /db_xref="HGNC:HGNC:28422"
                     /db_xref="MIM:608753"
     exon            1..401
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            402..607
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     CDS             419..1816
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /EC_number="4.6.1.16"
                     /note="isoform 1 is encoded by transcript variant 1;
                     tRNA-splicing endonuclease subunit Sen2; hsSen2;
                     tRNA-intron endonuclease Sen2; TSEN2 tRNA splicing
                     endonuclease subunit"
                     /codon_start=1
                     /product="tRNA-splicing endonuclease subunit Sen2 isoform
                     1"
                     /protein_id="NP_079541.1"
                     /db_xref="CCDS:CCDS2611.1"
                     /db_xref="GeneID:80746"
                     /db_xref="HGNC:HGNC:28422"
                     /db_xref="MIM:608753"
                     /translation="MAEAVFHAPKRKRRVYETYESPLPIPFGQDHGPLKEFKIFRAEM
                     INNNVIVRNAEDIEQLYGKGYFGKGILSRSRPSFTISDPKLVAKWKDMKTNMPIITSK
                     RYQHSVEWAAELMRRQGQDESTVRRILKDYTKPLEHPPVKRNEEAQVHDKLNSGMVSN
                     MEGTAGGERPSVVNGDSGKSGGVGDPREPLGCLQEGSGCHPTTESFEKSVREDASPLP
                     HVCCCKQDALILQRGLHHEDGSQHIGLLHPGDRGPDHEYVLVEEAECAMSEREAAPNE
                     ELVQRNRLICRRNPYRIFEYLQLSLEEAFFLVYALGCLSIYYEKEPLTIVKLWKAFTV
                     VQPTFRTTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASYSVIIELVDDHFE
                     GSLRRPLSWKSLAALSRVSVNVSKELMLCYLIKPSTMTDKEMESPECMKRIKVQEVIL
                     SRWVSSRERSDQDDL"
     exon            608..689
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            690..726
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            727..1249
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1250..1327
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1328..1378
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1379..1517
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1518..1554
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1555..1666
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1667..1756
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1757..2753
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2384..2389
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /note="hexamer: AATAAA"
     polyA_site      2408
                     /gene="TSEN2"
                     /gene_synonym="PCH2B; SEN2; SEN2L"
                     /note="major polyA site"
ORIGIN      
        1 gttgccgggg taacggcgag cgcgtggggc caagaaaggt aagggccctg ggcgaggaaa
       61 gcgcggccct ttccgagttt ggtgttttgc agcgaaagga aatctcgctc ttccgaaagt
      121 cctccagggc gagagaggaa agggcctagg tactgtgctg gggtcgcaca gccggccgag
      181 acagtgccgg gacggggagc caggcttccg agtgcgcccg gtcactgact cctccgcgct
      241 ttcctcgtgc gcctgcagcc cttggttctt ggaaacgccg gcgccttgtt cagggctggt
      301 ggggctgggg cgcaaggtgc agctgacaat gcccgagagg agccgcagcc tctggtggag
      361 ttcggtcggg tgtgggggta gtcaaggaaa gaagcaaagg gaatacctcc tctgaaaaat
      421 ggcagaagca gttttccatg ccccaaagag gaaaagaaga gtgtatgaga cttacgagtc
      481 tccattgcca atcccttttg gtcaggacca tggtcctctg aaagaattca agatattccg
      541 tgctgaaatg attaacaaca atgtgattgt gaggaatgcg gaggacattg agcagctcta
      601 tgggaaaggt tattttggaa aaggtattct ttcaagaagc cgtccaagct tcacaatttc
      661 agatcctaaa ctggttgcta aatggaaaga tatgaagaca aacatgccta tcatcacatc
      721 aaagaggtat cagcatagtg ttgagtgggc agcagagctg atgcgtagac aggggcagga
      781 tgagagtaca gtgcgcagaa tcctcaagga ttacacgaaa ccgcttgagc atcctcctgt
      841 gaaaaggaat gaagaggctc aagtgcatga caagcttaac tctggaatgg tttccaacat
      901 ggaaggcaca gcagggggag agagaccttc tgtggtaaac ggggactctg gaaagtcagg
      961 tggtgtgggt gatccccgtg agccattagg ctgcctgcag gagggctctg gctgccaccc
     1021 aacaacagag agctttgaga aaagcgtgcg agaggatgcc tcacctctgc cccatgtctg
     1081 ttgctgcaaa caagatgctc tcatcctcca gcgtggcctt catcatgaag acggcagcca
     1141 gcacatcggc ctcctgcatc ctggggacag agggcctgac catgagtacg tgctggtcga
     1201 ggaagcggag tgtgccatga gcgagaggga ggctgcccca aatgaggaat tggtgcaaag
     1261 aaacaggtta atatgcagaa gaaatccata taggatcttt gagtatttgc aactcagcct
     1321 agaagaggcc tttttcttgg tctatgctct gggatgttta agtatttact atgagaagga
     1381 gcctttaacg atagtgaagc tctggaaagc tttcactgta gttcagccca cgttcagaac
     1441 cacctacatg gcctaccatt actttcgaag caagggctgg gtgcccaaag tgggactcaa
     1501 gtacgggaca gatttactgc tatatcggaa aggccctcca ttttaccatg caagttattc
     1561 tgtcattatc gagctagttg atgaccattt tgaaggctct ctccgcaggc ctctcagttg
     1621 gaagtccctg gctgccttga gcagagtttc cgttaatgtc tctaaggaac ttatgctgtg
     1681 ctatttgatt aaaccctcta ctatgactga caaggaaatg gagtcaccag aatgtatgaa
     1741 aaggattaaa gttcaggagg tgattctgag tcgatgggtt tcttcacgag agaggagtga
     1801 ccaagacgat ctttaacaat tcaacctcaa atttctaatt tcaccaacaa ctatttattg
     1861 agggctaggt aaaaagttct ttttgttgta atcgtccatt aattcataag ttttaaaggg
     1921 catggtgctc ccagcaccag aaaactatca gtgtttttaa agataaatta cacaagggag
     1981 gagaaagatc cctgtgctag gactgcagat tctatacttg cgttggcctc taactctcca
     2041 atccagagcc tcctgcctct ggcgtcagtc ttttccctca tccactcact ggggagattg
     2101 gactagagga gtcctgagag gacacttcca acaagagaca tttattctct gattttacct
     2161 gaaaatggta gtagtttaca tttatacagt acagtttatg aagcactttc atacgcaggc
     2221 atctcttgtt acctacatct aagctgttcc cgaaagagtg ttacagaaca caacagtatt
     2281 gtacaatatt cgataagcat atcttcactg cacttgttat aaaaatgagt ggtgaaataa
     2341 tgtttggaga cataatgaaa gcgattaaca tttggcaaaa tataataaag cctttttgta
     2401 attggtgaga aagtcatgaa gacttaagtt gcctcagggc atctggtggc aagaggaggg
     2461 agatgggtgg ctgggcatgg tggcccatac ctataatccc agcacttggg aggccttggg
     2521 aggccaaggc gcatggatcg cttgagccca ggagttggag accagcttgg gcaacatggt
     2581 gaaacctcct ctctactaac aaaaattatc caagcattgt agcacatgcc tgtaattcca
     2641 gctgctcagg agactaaggt aggaggatcg cttgagccca ggaggaagag gttgcagtga
     2701 gcggagattg tgccactgca atccagcctg agcaatagag caaggtcctg tct
//
