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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

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