ID   TRM9B_HUMAN             Reviewed;         454 AA.
AC   Q9P272; K7EM26; Q8N9K7; Q96AW6;
DT   08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT   24-NOV-2009, sequence version 3.
DT   24-JAN-2024, entry version 140.
DE   RecName: Full=Probable tRNA methyltransferase 9B {ECO:0000305};
DE   AltName: Full=Probable tRNA methyltransferase 9-like protein {ECO:0000303|PubMed:23381944};
DE            EC=2.1.1.-;
GN   Name=TRMT9B {ECO:0000312|HGNC:HGNC:26725};
GN   Synonyms=C8orf79, KIAA1456, TRM9L {ECO:0000303|PubMed:23381944};
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=16421571; DOI=10.1038/nature04406;
RA   Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M.,
RA   Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L.,
RA   Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S.,
RA   Asakawa T., Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A.,
RA   Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III,
RA   Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K.,
RA   Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P.,
RA   Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H.,
RA   Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B.,
RA   O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K.,
RA   Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L.,
RA   Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G.,
RA   Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W.,
RA   Platzer M., Shimizu N., Lander E.S.;
RT   "DNA sequence and analysis of human chromosome 8.";
RL   Nature 439:331-335(2006).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   TISSUE=Cerebellum;
RX   PubMed=14702039; DOI=10.1038/ng1285;
RA   Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA   Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA   Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA   Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA   Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA   Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA   Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA   Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA   Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA   Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA   Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA   Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA   Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA   Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA   Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA   Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA   Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA   Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA   Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA   Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA   Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA   Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA   Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA   Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA   Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA   Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA   Isogai T., Sugano S.;
RT   "Complete sequencing and characterization of 21,243 full-length human
RT   cDNAs.";
RL   Nat. Genet. 36:40-45(2004).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 51-454 (ISOFORM 1), AND VARIANTS
RP   ARG-150; GLY-207; GLU-304 AND GLY-451.
RX   PubMed=10819331; DOI=10.1093/dnares/7.2.143;
RA   Nagase T., Kikuno R., Ishikawa K., Hirosawa M., Ohara O.;
RT   "Prediction of the coding sequences of unidentified human genes. XVII. The
RT   complete sequences of 100 new cDNA clones from brain which code for large
RT   proteins in vitro.";
RL   DNA Res. 7:143-150(2000).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 53-454 (ISOFORM 1), AND VARIANTS
RP   ARG-150; GLY-207; GLU-304 AND GLY-451.
RC   TISSUE=Eye;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   FUNCTION, AND TISSUE SPECIFICITY.
RX   PubMed=23381944; DOI=10.1002/emmm.201201161;
RA   Begley U., Sosa M.S., Avivar-Valderas A., Patil A., Endres L., Estrada Y.,
RA   Chan C.T., Su D., Dedon P.C., Aguirre-Ghiso J.A., Begley T.;
RT   "A human tRNA methyltransferase 9-like protein prevents tumour growth by
RT   regulating LIN9 and HIF1-alpha.";
RL   EMBO Mol. Med. 5:366-383(2013).
RN   [6]
RP   VARIANT PHE-93.
RX   PubMed=23647072; DOI=10.1111/epi.12201;
RA   Veeramah K.R., Johnstone L., Karafet T.M., Wolf D., Sprissler R.,
RA   Salogiannis J., Barth-Maron A., Greenberg M.E., Stuhlmann T., Weinert S.,
RA   Jentsch T.J., Pazzi M., Restifo L.L., Talwar D., Erickson R.P.,
RA   Hammer M.F.;
RT   "Exome sequencing reveals new causal mutations in children with epileptic
RT   encephalopathies.";
RL   Epilepsia 54:1270-1281(2013).
CC   -!- FUNCTION: May modify wobble uridines in specific arginine and glutamic
CC       acid tRNAs. Acts as a tumor suppressor by promoting the expression of
CC       LIN9. {ECO:0000269|PubMed:23381944}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q9P272-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q9P272-3; Sequence=VSP_059378, VSP_059379;
CC   -!- TISSUE SPECIFICITY: Down-regulated in breast, bladder, colorectal,
CC       cervix and testicular carcinomas. {ECO:0000269|PubMed:23381944}.
CC   -!- SIMILARITY: Belongs to the methyltransferase superfamily.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAC04326.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305};
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DR   EMBL; AC135352; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AB040889; BAA95980.1; -; mRNA.
DR   EMBL; BC035082; -; NOT_ANNOTATED_CDS; mRNA.
DR   EMBL; AK094299; BAC04326.1; ALT_SEQ; mRNA.
DR   EMBL; BC016633; AAH16633.2; -; mRNA.
DR   CCDS; CCDS47808.1; -. [Q9P272-1]
DR   RefSeq; NP_065895.2; NM_020844.2. [Q9P272-1]
DR   RefSeq; XP_005273643.1; XM_005273586.4.
DR   RefSeq; XP_016869194.1; XM_017013705.1.
DR   RefSeq; XP_016869195.1; XM_017013706.1.
DR   RefSeq; XP_016869196.1; XM_017013707.1.
DR   AlphaFoldDB; Q9P272; -.
DR   BioGRID; 121652; 7.
DR   IntAct; Q9P272; 2.
DR   STRING; 9606.ENSP00000432695; -.
DR   iPTMnet; Q9P272; -.
DR   PhosphoSitePlus; Q9P272; -.
DR   BioMuta; KIAA1456; -.
DR   DMDM; 269849677; -.
DR   MassIVE; Q9P272; -.
DR   PaxDb; 9606-ENSP00000432695; -.
DR   PeptideAtlas; Q9P272; -.
DR   ProteomicsDB; 83741; -. [Q9P272-1]
DR   Antibodypedia; 58596; 78 antibodies from 16 providers.
DR   DNASU; 57604; -.
DR   Ensembl; ENST00000400069.7; ENSP00000468715.1; ENSG00000250305.9. [Q9P272-3]
DR   Ensembl; ENST00000524591.7; ENSP00000432695.1; ENSG00000250305.9. [Q9P272-1]
DR   Ensembl; ENST00000528753.2; ENSP00000466330.1; ENSG00000250305.9. [Q9P272-3]
DR   GeneID; 57604; -.
DR   KEGG; hsa:57604; -.
DR   MANE-Select; ENST00000524591.7; ENSP00000432695.1; NM_020844.3; NP_065895.2.
DR   UCSC; uc010lsq.4; human. [Q9P272-1]
DR   UCSC; uc064kkg.1; human.
DR   AGR; HGNC:26725; -.
DR   CTD; 57604; -.
DR   DisGeNET; 57604; -.
DR   GeneCards; TRMT9B; -.
DR   HGNC; HGNC:26725; TRMT9B.
DR   HPA; ENSG00000250305; Group enriched (brain, choroid plexus, retina, thyroid gland).
DR   MIM; 615666; gene.
DR   neXtProt; NX_Q9P272; -.
DR   OpenTargets; ENSG00000250305; -.
DR   PharmGKB; PA143485343; -.
DR   VEuPathDB; HostDB:ENSG00000250305; -.
DR   eggNOG; KOG1331; Eukaryota.
DR   GeneTree; ENSGT00940000160373; -.
DR   HOGENOM; CLU_029501_0_1_1; -.
DR   InParanoid; Q9P272; -.
DR   OMA; HGNWCIV; -.
DR   OrthoDB; 5473013at2759; -.
DR   PhylomeDB; Q9P272; -.
DR   PathwayCommons; Q9P272; -.
DR   Reactome; R-HSA-6782315; tRNA modification in the nucleus and cytosol.
DR   SignaLink; Q9P272; -.
DR   BioGRID-ORCS; 57604; 14 hits in 1135 CRISPR screens.
DR   GenomeRNAi; 57604; -.
DR   Pharos; Q9P272; Tbio.
DR   PRO; PR:Q9P272; -.
DR   Proteomes; UP000005640; Chromosome 8.
DR   RNAct; Q9P272; Protein.
DR   Bgee; ENSG00000250305; Expressed in cerebellar vermis and 153 other cell types or tissues.
DR   ExpressionAtlas; Q9P272; baseline and differential.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0008757; F:S-adenosylmethionine-dependent methyltransferase activity; IEA:InterPro.
DR   GO; GO:0106335; F:tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity; IBA:GO_Central.
DR   GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR   GO; GO:0008175; F:tRNA methyltransferase activity; EXP:Reactome.
DR   GO; GO:0030488; P:tRNA methylation; IBA:GO_Central.
DR   GO; GO:0006400; P:tRNA modification; TAS:Reactome.
DR   GO; GO:0002098; P:tRNA wobble uridine modification; IBA:GO_Central.
DR   CDD; cd02440; AdoMet_MTases; 1.
DR   Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 2.
DR   InterPro; IPR013216; Methyltransf_11.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   PANTHER; PTHR13069:SF36; TRNA METHYLTRANSFERASE 9B-RELATED; 1.
DR   PANTHER; PTHR13069; UNCHARACTERIZED; 1.
DR   Pfam; PF08241; Methyltransf_11; 1.
DR   SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR   Genevisible; Q9P272; HS.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Methyltransferase; Phosphoprotein;
KW   Reference proteome; S-adenosyl-L-methionine; Transferase; tRNA processing.
FT   CHAIN           1..454
FT                   /note="Probable tRNA methyltransferase 9B"
FT                   /id="PRO_0000328792"
FT   MOD_RES         214
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:Q80WQ4"
FT   VAR_SEQ         53..60
FT                   /note="CGTGKYLK -> NQAASSLT (in isoform 2)"
FT                   /id="VSP_059378"
FT   VAR_SEQ         61..454
FT                   /note="Missing (in isoform 2)"
FT                   /id="VSP_059379"
FT   VARIANT         93
FT                   /note="L -> F (found in a child with sporadic epilepsy;
FT                   uncertain significance; dbSNP:rs757023992)"
FT                   /evidence="ECO:0000269|PubMed:23647072"
FT                   /id="VAR_077832"
FT   VARIANT         150
FT                   /note="H -> R (in dbSNP:rs528255)"
FT                   /evidence="ECO:0000269|PubMed:10819331,
FT                   ECO:0000269|PubMed:15489334"
FT                   /id="VAR_061378"
FT   VARIANT         207
FT                   /note="C -> G (in dbSNP:rs3739310)"
FT                   /evidence="ECO:0000269|PubMed:10819331,
FT                   ECO:0000269|PubMed:15489334"
FT                   /id="VAR_061379"
FT   VARIANT         219
FT                   /note="P -> T (in dbSNP:rs505480)"
FT                   /id="VAR_056243"
FT   VARIANT         265
FT                   /note="I -> T (in dbSNP:rs3739308)"
FT                   /id="VAR_056244"
FT   VARIANT         304
FT                   /note="G -> E (in dbSNP:rs502882)"
FT                   /evidence="ECO:0000269|PubMed:10819331,
FT                   ECO:0000269|PubMed:15489334"
FT                   /id="VAR_061380"
FT   VARIANT         337
FT                   /note="H -> L (in dbSNP:rs34995506)"
FT                   /id="VAR_056245"
FT   VARIANT         451
FT                   /note="R -> G (in dbSNP:rs608052)"
FT                   /evidence="ECO:0000269|PubMed:10819331,
FT                   ECO:0000269|PubMed:15489334"
FT                   /id="VAR_061381"
SQ   SEQUENCE   454 AA;  51299 MW;  72074CFF852A0331 CRC64;
     MDHEAAQLEK QHVHNVYEST APYFSDLQSK AWPRVRQFLQ EQKPGSLIAD IGCGTGKYLK
     VNSQVHTVGC DYCGPLVEIA RNRGCEAMVC DNLNLPFRDE GFDAIISIGV IHHFSTKQRR
     IRAIKEMARV LVPGGQLMIY VWAMEQKNRH FEKQDVLVPW NRALCSQLFS ESSQSGRKRQ
     CGYPERGHPY HPPCSECSCS VCFKEQCGSK RSHSVGYEPA MARTCFANIS KEGEEEYGFY
     STLGKSFRSW FFSRSLDEST LRKQIERVRP LKNTEVWASS TVTVQPSRHS SLDFDHQEPF
     STKGQSLDEE VFVESSSGKH LEWLRAPGTL KHLNGDHQGE MRRNGGGNFL DSTNTGVNCV
     DAGNIEDDNP SASKILRRIS AVDSTDFNPD DTMSVEDPQT DVLDSTAFMR YYHVFREGEL
     CSLLKENVSE LRILSSGNDH GNWCIIAEKK RGCD
//