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    TRMT10B tRNA methyltransferase 10B [ Homo sapiens (human) ]

    Gene ID: 158234, updated on 3-Apr-2024

    Summary

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    Official Symbol
    TRMT10Bprovided by HGNC
    Official Full Name
    tRNA methyltransferase 10Bprovided by HGNC
    Primary source
    HGNC:HGNC:26454
    See related
    Ensembl:ENSG00000165275 AllianceGenome:HGNC:26454
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RG9MTD3; bA3J10.9
    Summary
    Enables tRNA (guanine-N1-)-methyltransferase activity. Predicted to be involved in mitochondrial tRNA processing. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in endometrium (RPKM 2.9), brain (RPKM 2.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9p13.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (37752901..37778972)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37776617..37802703)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (37753802..37778969)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene FERM and PDZ domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19911 Neighboring gene RAB1C, member RAS oncogene family (pseudogene) Neighboring gene RN7SK pseudogene 171 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:37697369-37697615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37745887-37746388 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:37753712-37753946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28402 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:37784801-37785316 Neighboring gene uncharacterized LOC105376037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37800323-37800924 Neighboring gene exosome component 3 Neighboring gene DDB1 and CUL4 associated factor 10

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B. Vilardo E, et al. Nucleic Acids Res, 2020 Jun 19. PMID 32392304, Free PMC Article
    2. Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B. Howell NW, et al. RNA, 2019 Oct. PMID 31292261, Free PMC Article
    3. Cryo-EM structure of the human mitochondrial translocase TIM22 complex. Qi L, et al. Cell Res, 2021 Mar. PMID 32901109, Free PMC Article
    4. A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis. Vilardo E, et al. Nucleic Acids Res, 2012 Dec. PMID 23042678, Free PMC Article
    5. The gluconeogenic enzyme PCK1 phosphorylates INSIG1/2 for lipogenesis. Xu D, et al. Nature, 2020 Apr. PMID 32322062

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B.
      Title: Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B.
    2. demonstrate that human TRMT10A (hTRMT10A) and human TRMT10B (hTRMT10B) are not biochemically redundant
      Title: Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ31455

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA (guanosine(9)-N1)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein insertion into mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA N1-guanine methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of TIM22 mitochondrial import inner membrane insertion complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    tRNA methyltransferase 10 homolog B
    Names
    RNA (guanine-9-) methyltransferase domain containing 3
    RNA (guanine-9-)-methyltransferase domain-containing protein 3
    tRNA (guanine(9)-N(1))-methyltransferase TRMT10B
    NP_001273879.1
    NP_001273880.1
    NP_001273881.1
    NP_001273882.1
    NP_001273883.1
    NP_659401.2
    XP_005251432.1
    XP_011516037.1
    XP_011516038.1
    XP_011516040.1
    XP_011516041.1
    XP_011516044.1
    XP_016869802.1
    XP_024303194.1
    XP_047278789.1
    XP_047278790.1
    XP_054218054.1
    XP_054218055.1
    XP_054218056.1
    XP_054218057.1
    XP_054218058.1
    XP_054218059.1
    XP_054218060.1
    XP_054218061.1
    XP_054218062.1
    XP_054218063.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001286950.2 → NP_001273879.1  tRNA methyltransferase 10 homolog B isoform b

      See identical proteins and their annotated locations for NP_001273879.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AK056017, AK092718, AK295733, CA440955, HY066525
      Consensus CDS
      CCDS69598.1
      UniProtKB/Swiss-Prot
      Q6PF06
      Related
      ENSP00000444997.1, ENST00000537911.5
      Conserved Domains (1) summary
      cl00407
      Location:144 → 247
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    2. NM_001286951.2 → NP_001273880.1  tRNA methyltransferase 10 homolog B isoform c

      See identical proteins and their annotated locations for NP_001273880.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' region, resulting in an alternate 5' UTR and translation initiation from an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AK056017, AK092718, BC057774, CA440955, HY066525
      Consensus CDS
      CCDS69601.1
      UniProtKB/Swiss-Prot
      Q6PF06
      Related
      ENSP00000366983.2, ENST00000377754.6
      Conserved Domains (1) summary
      cl00407
      Location:41 → 212
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    3. NM_001286952.2 → NP_001273881.1  tRNA methyltransferase 10 homolog B isoform d

      See identical proteins and their annotated locations for NP_001273881.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate exons that result in the loss of an in-frame segment in the 5' coding region, and it uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AK056017, AK092718, AK294219, BC057774, CA440955, HY066525
      Consensus CDS
      CCDS69600.1
      UniProtKB/Swiss-Prot
      Q6PF06
      Related
      ENSP00000366982.2, ENST00000377753.6
      Conserved Domains (1) summary
      cl00407
      Location:62 → 220
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    4. NM_001286953.2 → NP_001273882.1  tRNA methyltransferase 10 homolog B isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in its 5' UTR, initiates translation from an alternate start codon, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (e) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AK056017, AK092718, AK315922, BC057774, CA440955, HY066525
      UniProtKB/TrEMBL
      B7Z9F7
      Conserved Domains (1) summary
      cd18100
      Location:33 → 187
      Trm10euk_B; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog B

    5. NM_001286954.2 → NP_001273883.1  tRNA methyltransferase 10 homolog B isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks an exon and uses an alternate splice site in the central region, and it thus differs in its 5' UTR and initiates translation from an alternate start codon, and it uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (f) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AK056017, AK092718, BC057774, CA440955, CR986760, HY066525
      UniProtKB/Swiss-Prot
      Q6PF06
      Conserved Domains (1) summary
      cl00407
      Location:84 → 187
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    6. NM_144964.4 → NP_659401.2  tRNA methyltransferase 10 homolog B isoform a

      See identical proteins and their annotated locations for NP_659401.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AK056017, AK092718, BC057774, CA440955, HY066525
      Consensus CDS
      CCDS43804.1
      UniProtKB/Swiss-Prot
      B7Z216, B7Z3D3, Q05DJ4, Q5QP83, Q6PF06, Q8NAG2, Q96N36
      Related
      ENSP00000297994.3, ENST00000297994.4
      Conserved Domains (1) summary
      cl00407
      Location:136 → 307
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    RNA

    1. NR_104612.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK056017, AK092718, AK304516, BC057774, CA440955, HY066525

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      37752901..37778972
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011517735.4 → XP_011516037.1  tRNA methyltransferase 10 homolog B isoform X1

      Conserved Domains (1) summary
      cl00407
      Location:149 → 320
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    2. XM_011517736.4 → XP_011516038.1  tRNA methyltransferase 10 homolog B isoform X2

      Conserved Domains (1) summary
      cl00407
      Location:149 → 311
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    3. XM_011517738.3 → XP_011516040.1  tRNA methyltransferase 10 homolog B isoform X6

      Conserved Domains (1) summary
      cl00407
      Location:75 → 242
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    4. XM_011517739.4 → XP_011516041.1  tRNA methyltransferase 10 homolog B isoform X7

      Conserved Domains (1) summary
      cl00407
      Location:75 → 233
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    5. XM_017014313.3 → XP_016869802.1  tRNA methyltransferase 10 homolog B isoform X5

    6. XM_047422833.1 → XP_047278789.1  tRNA methyltransferase 10 homolog B isoform X4

    7. XM_011517742.2 → XP_011516044.1  tRNA methyltransferase 10 homolog B isoform X9

      See identical proteins and their annotated locations for XP_011516044.1

      UniProtKB/TrEMBL
      B7Z968
      Related
      ENSP00000437395.1, ENST00000488673.6

    8. XM_024447426.2 → XP_024303194.1  tRNA methyltransferase 10 homolog B isoform X3

      Conserved Domains (1) summary
      cl00407
      Location:136 → 298
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    9. XM_005251375.3 → XP_005251432.1  tRNA methyltransferase 10 homolog B isoform X8

      Conserved Domains (1) summary
      cl00407
      Location:62 → 229
      tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

    10. XM_047422834.1 → XP_047278790.1  tRNA methyltransferase 10 homolog B isoform X10

    RNA

    1. XR_007061248.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      37776617..37802703
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362079.1 → XP_054218054.1  tRNA methyltransferase 10 homolog B isoform X1

    2. XM_054362083.1 → XP_054218058.1  tRNA methyltransferase 10 homolog B isoform X5

    3. XM_054362087.1 → XP_054218062.1  tRNA methyltransferase 10 homolog B isoform X9

    4. XM_054362085.1 → XP_054218060.1  tRNA methyltransferase 10 homolog B isoform X7

    5. XM_054362082.1 → XP_054218057.1  tRNA methyltransferase 10 homolog B isoform X4

    6. XM_054362080.1 → XP_054218055.1  tRNA methyltransferase 10 homolog B isoform X2

    7. XM_054362084.1 → XP_054218059.1  tRNA methyltransferase 10 homolog B isoform X6

    8. XM_054362081.1 → XP_054218056.1  tRNA methyltransferase 10 homolog B isoform X3

    9. XM_054362086.1 → XP_054218061.1  tRNA methyltransferase 10 homolog B isoform X8

    10. XM_054362088.1 → XP_054218063.1  tRNA methyltransferase 10 homolog B isoform X10

    RNA

    1. XR_008487945.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PF06.1 GenPept UniProtKB/Swiss-Prot:Q6PF06

    Gene LinkOut

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