LOCUS       NM_016408               2080 bp    mRNA    linear   PRI 19-JAN-2025
DEFINITION  Homo sapiens CDK5RAP1 mitochondrial tRNA methylthiotransferase
            (CDK5RAP1), transcript variant 1, mRNA; nuclear gene for
            mitochondrial product.
ACCESSION   NM_016408
VERSION     NM_016408.4
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 2080)
  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   2  (bases 1 to 2080)
  AUTHORS   Adami,R. and Bottai,D.
  TITLE     S-adenosylmethionine tRNA modification: unexpected/unsuspected
            implications of former/new players
  JOURNAL   Int J Biol Sci 16 (15), 3018-3027 (2020)
   PUBMED   33061813
  REMARK    Review article
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2080)
  AUTHORS   Fakruddin,M., Wei,F.Y., Emura,S., Matsuda,S., Yasukawa,T., Kang,D.
            and Tomizawa,K.
  TITLE     Cdk5rap1-mediated 2-methylthio-N6-isopentenyladenosine modification
            is absent from nuclear-derived RNA species
  JOURNAL   Nucleic Acids Res 45 (20), 11954-11961 (2017)
   PUBMED   28981754
  REMARK    GeneRIF: The mitochondrial localization of ms2i6A modification was
            diminished in HeLa cells when transfected with siRNA against Cdk5
            regulatory subunit-associated protein 1 (Cdk5rap1), suggesting that
            the modification occurs in tRNAs in mitochondria.
REFERENCE   4  (bases 1 to 2080)
  AUTHORS   Yang,X., Coulombe-Huntington,J., Kang,S., Sheynkman,G.M., Hao,T.,
            Richardson,A., Sun,S., Yang,F., Shen,Y.A., Murray,R.R., Spirohn,K.,
            Begg,B.E., Duran-Frigola,M., MacWilliams,A., Pevzner,S.J.,
            Zhong,Q., Wanamaker,S.A., Tam,S., Ghamsari,L., Sahni,N., Yi,S.,
            Rodriguez,M.D., Balcha,D., Tan,G., Costanzo,M., Andrews,B.,
            Boone,C., Zhou,X.J., Salehi-Ashtiani,K., Charloteaux,B., Chen,A.A.,
            Calderwood,M.A., Aloy,P., Roth,F.P., Hill,D.E., Iakoucheva,L.M.,
            Xia,Y. and Vidal,M.
  TITLE     Widespread Expansion of Protein Interaction Capabilities by
            Alternative Splicing
  JOURNAL   Cell 164 (4), 805-817 (2016)
   PUBMED   26871637
REFERENCE   5  (bases 1 to 2080)
  AUTHORS   Reiter,V., Matschkal,D.M., Wagner,M., Globisch,D.,
            Kneuttinger,A.C., Muller,M. and Carell,T.
  TITLE     The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on
            nuclear and mitochondrial RNA
  JOURNAL   Nucleic Acids Res 40 (13), 6235-6240 (2012)
   PUBMED   22422838
  REMARK    GeneRIF: CDK5RAP1 is a radical SAM enzyme, which postsynthetically
            converts the RNA modification N6-isopentenyladenosine into
            2-methylthio-N6-isopentenyladenosine.
REFERENCE   6  (bases 1 to 2080)
  AUTHORS   Oh,J.H., Yang,J.O., Hahn,Y., Kim,M.R., Byun,S.S., Jeon,Y.J.,
            Kim,J.M., Song,K.S., Noh,S.M., Kim,S., Yoo,H.S., Kim,Y.S. and
            Kim,N.S.
  TITLE     Transcriptome analysis of human gastric cancer
  JOURNAL   Mamm Genome 16 (12), 942-954 (2005)
   PUBMED   16341674
REFERENCE   7  (bases 1 to 2080)
  AUTHORS   Zou,X., Ji,C., Jin,F., Liu,J., Wu,M., Zheng,H., Wang,Y., Li,X.,
            Xu,J., Gu,S., Xie,Y. and Mao,Y.
  TITLE     Cloning, characterization and expression of CDK5RAP1_v3 and
            CDK5RAP1_v4, two novel splice variants of human CDK5RAP1
  JOURNAL   Genes Genet Syst 79 (3), 177-182 (2004)
   PUBMED   15329498
REFERENCE   8  (bases 1 to 2080)
  AUTHORS   Ching,Y.P., Pang,A.S., Lam,W.H., Qi,R.Z. and Wang,J.H.
  TITLE     Identification of a neuronal Cdk5 activator-binding protein as Cdk5
            inhibitor
  JOURNAL   J Biol Chem 277 (18), 15237-15240 (2002)
   PUBMED   11882646
REFERENCE   9  (bases 1 to 2080)
  AUTHORS   Wang,X., Ching,Y.P., Lam,W.H., Qi,Z., Zhang,M. and Wang,J.H.
  TITLE     Identification of a common protein association region in the
            neuronal Cdk5 activator
  JOURNAL   J Biol Chem 275 (41), 31763-31769 (2000)
   PUBMED   10915792
REFERENCE   10 (bases 1 to 2080)
  AUTHORS   Ching,Y.P., Qi,Z. and Wang,J.H.
  TITLE     Cloning of three novel neuronal Cdk5 activator binding proteins
  JOURNAL   Gene 242 (1-2), 285-294 (2000)
   PUBMED   10721722
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK314532.1, DA028522.1 and
            AA721451.1.
            
            On Nov 22, 2018 this sequence version replaced NM_016408.3.
            
            Summary: This gene encodes a regulator of cyclin-dependent kinase 5
            activity. This protein has also been reported to modify RNA by
            adding a methylthio-group and may thus have a dual function as an
            RNA methylthiotransferase and as an inhibitor of cyclin-dependent
            kinase 5 activity. Alternative splicing results in multiple
            transcript variants that encode different isoforms. [provided by
            RefSeq, May 2013].
            
            Transcript Variant: This variant (1) encodes isoform (a).
            
            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 :: SRR3476690.976177.1,
                                           SRR3476690.631529.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            gene product(s) localized to mito. :: PMID: 22422838
            MANE Ensembl match                 :: ENST00000346416.7/
                                                  ENSP00000217372.2
            RefSeq Select criteria             :: based on conservation,
                                                  expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-543               AK314532.1         1-543
            544-573             DA028522.1         544-573
            574-1876            AK314532.1         574-1876
            1877-2080           AA721451.1         14-217              c
FEATURES             Location/Qualifiers
     source          1..2080
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20q11.21"
     gene            1..2080
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /note="CDK5RAP1 mitochondrial tRNA methylthiotransferase"
                     /db_xref="GeneID:51654"
                     /db_xref="HGNC:HGNC:15880"
                     /db_xref="MIM:608200"
     exon            1..92
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            93..416
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     CDS             113..1876
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /EC_number="2.8.4.3"
                     /note="isoform a is encoded by transcript variant 1; CDK5
                     activator-binding protein C42;
                     mt-tRNA-2-methylthio-N6-dimethylallyladenosine synthase;
                     mt-tRNA-N6-(dimethylallyl)adenosine(37)
                     methylthiotransferase; mitochondrial tRNA
                     methylthiotransferase CDK5RAP1; CDK5 regulatory subunit
                     associated protein 1"
                     /codon_start=1
                     /product="mitochondrial tRNA methylthiotransferase
                     CDK5RAP1 isoform a"
                     /protein_id="NP_057492.2"
                     /db_xref="CCDS:CCDS13219.1"
                     /db_xref="GeneID:51654"
                     /db_xref="HGNC:HGNC:15880"
                     /db_xref="MIM:608200"
                     /translation="MHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSP
                     ERQEDGARKDFSSRLAAGPTFQHFLKSASAPQEKLSSEVEDPPPYLMMDELLGRQRKV
                     YLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLH
                     QLKALKTRRPRSRVPLRIGILGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVA
                     ESGQQAANVLLSLDETYADVMPVQTSASATSAFVSIMRGCDNMCSYCIVPFTRGRERS
                     RPIASILEEVKKLSEQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTK
                     QGGLRFAHLLDQVSRVDPEMRIRFTSPHPKDFPDEVLQLIHERDNICKQIHLPAQSGS
                     SRVLEAMRRGYSREAYVELVHHIRESIPGVSLSSDFIAGFCGETEEDHVQTVSLLREV
                     QYNMGFLFAYSMRQKTRAYHRLKDDVPEEVKLRRLEELITIFREEATKANQTSVGCTQ
                     LVLVEGLSKRSATDLCGRNDGNLKVIFPDAEMEDVNNPGLRVRAQPGDYVLVKITSAS
                     SQTLRGHVLCRTTLRDSSAYC"
     exon            417..520
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            521..555
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            556..656
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            657..867
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            868..988
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            989..1219
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            1220..1317
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            1318..1373
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            1374..1504
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            1505..1654
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            1655..1795
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     exon            1796..2080
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2055..2060
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /note="hexamer: ATTAAA"
     polyA_site      2080
                     /gene="CDK5RAP1"
                     /gene_synonym="C20orf34; C42; CGI-05; HSPC167"
                     /note="major polyA site"
ORIGIN      
        1 gtgtatgaac gcagcggcgg acctgtgagg ggatccgact tgccggcaga acttacgctg
       61 cgggaccccg ggcactgttg ctgctgcggg agactgtggg ctgtttagtg ccatgcaccc
      121 tttacagtgt gtcctccaag tgcagaggtc tctggggtgg ggaccattgg cctctgtgtc
      181 ttggctgtcg ctgaggatgt gcagggcaca cagcagtctc tctagtacca tgtgtcccag
      241 tccagagagg caggaggatg gagctcggaa ggatttcagc tccaggctgg ctgctggacc
      301 gacttttcaa cattttttaa aaagtgcctc agctcctcag gagaagctgt cttcagaagt
      361 ggaagaccca cctccctatc tcatgatgga tgaacttctt ggaaggcaga gaaaagtcta
      421 cctcgagacc tatggctgcc agatgaatgt gaatgacaca gagatagcct ggtccatctt
      481 acagaagagt ggctacctgc ggaccagtaa cctccaagag gcagatgtga ttctccttgt
      541 cacatgctct atcagggaga aggctgagca gaccatctgg aaccgtttac atcagcttaa
      601 agccttgaag acaaggcggc cccgctcccg ggttcctctg aggattggaa ttctaggctg
      661 catggctgag aggttgaagg aggagattct caacagagag aaaatggtag atattttggc
      721 tggtcctgat gcctaccggg accttccccg gctgctggct gttgctgagt cgggccagca
      781 agctgccaac gtgctgctct ctctggacga gacctatgct gatgtcatgc cagtccagac
      841 aagcgccagt gccacgtctg cctttgtgtc aatcatgcga ggctgtgaca acatgtgtag
      901 ctactgcatt gttcctttca cccggggcag ggagaggagt cggcctattg cctccattct
      961 agaggaagtg aagaagcttt ctgagcaggg gctgaaagaa gtgacacttc ttggtcagaa
     1021 tgttaatagt tttcgggaca attcggaggt ccagttcaac agtgcagtgc ctaccaatct
     1081 cagtcgtggc tttaccacca actataaaac caagcaagga ggacttcgtt ttgctcatct
     1141 tctggatcag gtctccagag tagatcctga aatgaggatc cgttttacct ctccccaccc
     1201 caaggatttt cctgatgagg ttctgcagct gattcatgag agagataaca tctgtaaaca
     1261 gatccacctg ccagcccaga gtggaagcag ccgtgtgttg gaggccatgc ggaggggata
     1321 ttcaagagaa gcttatgtgg agttagttca ccatattaga gaatctattc caggtgtgag
     1381 cctcagcagc gatttcattg ctggcttttg tggtgagacg gaggaagatc acgtccagac
     1441 agtctctttg ctccgggaag ttcagtacaa catgggcttc ctctttgcct acagcatgag
     1501 acagaagaca cgggcatatc ataggctgaa ggatgatgtc ccggaagagg taaaattaag
     1561 gcgtttggag gaactcatca ctatcttccg agaagaagca acaaaagcca atcagacctc
     1621 tgtgggctgt acccagttgg tgctagtgga agggctcagt aaacgctctg ccactgacct
     1681 gtgtggcagg aatgatggaa accttaaggt gatcttccct gatgcagaga tggaggatgt
     1741 caataaccct gggctcaggg tcagagccca gcctggggac tatgtgctgg tgaagatcac
     1801 ctcagccagt tctcagacac ttaggggaca tgttctctgc aggaccactc tgagggactc
     1861 ttctgcatat tgctgacctg agaggatggc ctcagagctg acttgggcaa tcctccccaa
     1921 caggaagggg agacattgcc tgccactgag gaaacaggtc atgaaggtgg agataagctg
     1981 caaggggcga agcaacttta tgtcagtgga aaacgtgtct ctttaaagct gctatgtgaa
     2041 cagcttttac agtcattaaa tttacctaaa ctaaggttaa
//
