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TRMT2B tRNA methyltransferase 2 homolog B [ Homo sapiens (human) ]

Gene ID: 79979, updated on 3-Apr-2024

Summary

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Official Symbol
TRMT2Bprovided by HGNC
Official Full Name
tRNA methyltransferase 2 homolog Bprovided by HGNC
Primary source
HGNC:HGNC:25748
See related
Ensembl:ENSG00000188917 AllianceGenome:HGNC:25748
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CXorf34; dJ341D10.3
Summary
This gene encodes a homolog of the TRM2 gene in S. cerevisiae. The yeast gene encodes a tRNA methyltransferase that plays a role in tRNA maturation. The yeast protein also has endo-exonuclease activity and may be involved in DNA double strand break repair. Alternative splicing results in multiple transcripts encoding different isoforms. [provided by RefSeq, Nov 2009]
Expression
Ubiquitous expression in thyroid (RPKM 3.4), spleen (RPKM 3.4) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See TRMT2B in Genome Data Viewer
Location:
Xq22.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (100973366..101052111, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (99416819..99495549, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (100264339..100307100, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene XK related X-linked Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:100182110-100183309 Neighboring gene NSA2 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29806 Neighboring gene CSGALNACT2 pseudogene 1 Neighboring gene ADP ribosylation factor like GTPase 13A Neighboring gene ReSE screen-validated silencer GRCh37_chrX:100246331-100246526 Neighboring gene uncharacterized LOC124905285 Neighboring gene transmembrane protein 35A

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. TRMT2B is responsible for both tRNA and rRNA m(5)U-methylation in human mitochondria. Powell CA, et al. RNA Biol, 2020 Apr. PMID 31948311, Free PMC Article
  2. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Dai W, et al. Nat Chem Biol, 2021 Nov. PMID 34556860, Free PMC Article
  3. APEX Fingerprinting Reveals the Subcellular Localization of Proteins of Interest. Lee SY, et al. Cell Rep, 2016 May 24. PMID 27184847
  4. Systematic interactome mapping of acute lymphoblastic leukemia cancer gene products reveals EXT-1 tumor suppressor as a Notch1 and FBWX7 common interactor. Daakour S, et al. BMC Cancer, 2016 May 26. PMID 27229929, Free PMC Article
  5. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Floyd BJ, et al. Mol Cell, 2016 Aug 18. PMID 27499296, Free PMC Article

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRMT2B is responsible for both tRNA and rRNA m(5)U-methylation in human mitochondria.
    Title: TRMT2B is responsible for both tRNA and rRNA m(5)U-methylation in human mitochondria.
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

  • FLJ12687

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables rRNA (uridine-C5-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in rRNA methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in mitochondrial matrix IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
tRNA (uracil-5-)-methyltransferase homolog B
Names
TRM2 homolog
TRM2 homolog B
TRM2 tRNA methyltransferase 2 homolog B
rRNA (uracil-5-)-methyltransferase TRMT2B
tRNA (uracil(54)-C(5))-methyltransferase homolog
tRNA (uracil-5-)-methyltransferase homolog
NP_001161442.1
NP_001161443.1
NP_001161444.1
NP_079193.2
XP_005262253.1
XP_005262258.1
XP_011529344.1
XP_016885354.1
XP_016885359.1
XP_047298488.1
XP_047298489.1
XP_047298490.1
XP_054183882.1
XP_054183883.1
XP_054183884.1
XP_054183885.1
XP_054183886.1
XP_054183887.1
XP_054183888.1
XP_054183889.1

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.

Genomic

  1. NG_015971.2 RefSeqGene

    Range
    5000..47761
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001167970.2 → NP_001161442.1  tRNA (uracil-5-)-methyltransferase homolog B isoform a

    See identical proteins and their annotated locations for NP_001161442.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 4 all encode isoform a.
    Source sequence(s)
    BC020116, DA391184, DA454040, Z97985
    Consensus CDS
    CCDS14477.1
    UniProtKB/Swiss-Prot
    A6NDG5, A6NEI9, A6NMG6, Q5JPF0, Q5JVY6, Q96GJ1, Q96HU7, Q96IH9, Q9H9K2
    UniProtKB/TrEMBL
    B2RE31
    Related
    ENSP00000362026.1, ENST00000372935.5
    Conserved Domains (2) summary
    COG2265
    Location:94 → 497
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:298 → 501
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  2. NM_001167971.2 → NP_001161443.1  tRNA (uracil-5-)-methyltransferase homolog B isoform b

    See identical proteins and their annotated locations for NP_001161443.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. It encodes isoform b, which is shorter than isoform a.
    Source sequence(s)
    AL832849, BG747665, DA454040, Z97985
    Consensus CDS
    CCDS55464.1
    UniProtKB/TrEMBL
    B2RE31
    Related
    ENSP00000362030.1, ENST00000372939.5
    Conserved Domains (2) summary
    COG2265
    Location:106 → 452
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:253 → 456
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  3. NM_001167972.2 → NP_001161444.1  tRNA (uracil-5-)-methyltransferase homolog B isoform a

    See identical proteins and their annotated locations for NP_001161444.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 4 all encode isoform a.
    Source sequence(s)
    BC009437, BX647969, Z97985
    Consensus CDS
    CCDS14477.1
    UniProtKB/Swiss-Prot
    A6NDG5, A6NEI9, A6NMG6, Q5JPF0, Q5JVY6, Q96GJ1, Q96HU7, Q96IH9, Q9H9K2
    UniProtKB/TrEMBL
    B2RE31
    Related
    ENSP00000438134.1, ENST00000545398.5
    Conserved Domains (2) summary
    COG2265
    Location:94 → 497
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:298 → 501
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  4. NM_024917.6 → NP_079193.2  tRNA (uracil-5-)-methyltransferase homolog B isoform a

    See identical proteins and their annotated locations for NP_079193.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 4 all encode isoform a.
    Source sequence(s)
    BC034272, DA454040, Z97985
    Consensus CDS
    CCDS14477.1
    UniProtKB/Swiss-Prot
    A6NDG5, A6NEI9, A6NMG6, Q5JPF0, Q5JVY6, Q96GJ1, Q96HU7, Q96IH9, Q9H9K2
    UniProtKB/TrEMBL
    B2RE31
    Related
    ENSP00000362027.3, ENST00000372936.4
    Conserved Domains (2) summary
    COG2265
    Location:94 → 497
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:298 → 501
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    100973366..101052111 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005262196.3 → XP_005262253.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X1

    See identical proteins and their annotated locations for XP_005262253.1

    UniProtKB/Swiss-Prot
    A6NDG5, A6NEI9, A6NMG6, Q5JPF0, Q5JVY6, Q96GJ1, Q96HU7, Q96IH9, Q9H9K2
    UniProtKB/TrEMBL
    B2RE31
    Conserved Domains (2) summary
    COG2265
    Location:94 → 497
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:298 → 501
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  2. XM_011531042.3 → XP_011529344.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X3

    See identical proteins and their annotated locations for XP_011529344.1

    Conserved Domains (2) summary
    COG2265
    Location:23 → 378
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:179 → 382
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  3. XM_005262201.3 → XP_005262258.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X4

    See identical proteins and their annotated locations for XP_005262258.1

    Conserved Domains (1) summary
    cl27845
    Location:59 → 258
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]

  4. XM_017029870.2 → XP_016885359.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X3

    Conserved Domains (2) summary
    COG2265
    Location:23 → 378
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:179 → 382
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  5. XM_017029865.2 → XP_016885354.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X3

    Conserved Domains (2) summary
    COG2265
    Location:23 → 378
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:179 → 382
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  6. XM_047442532.1 → XP_047298488.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X1

    UniProtKB/Swiss-Prot
    A6NDG5, A6NEI9, A6NMG6, Q5JPF0, Q5JVY6, Q96GJ1, Q96HU7, Q96IH9, Q9H9K2

  7. XM_047442534.1 → XP_047298490.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X3

  8. XM_047442533.1 → XP_047298489.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X2

RNA

  1. XR_001755729.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    99416819..99495549 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327908.1 → XP_054183883.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X1

    UniProtKB/Swiss-Prot
    A6NDG5, A6NEI9, A6NMG6, Q5JPF0, Q5JVY6, Q96GJ1, Q96HU7, Q96IH9, Q9H9K2

  2. XM_054327913.1 → XP_054183888.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X3

  3. XM_054327914.1 → XP_054183889.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X4

  4. XM_054327911.1 → XP_054183886.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X3

  5. XM_054327910.1 → XP_054183885.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X3

  6. XM_054327907.1 → XP_054183882.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X1

    UniProtKB/Swiss-Prot
    A6NDG5, A6NEI9, A6NMG6, Q5JPF0, Q5JVY6, Q96GJ1, Q96HU7, Q96IH9, Q9H9K2

  7. XM_054327912.1 → XP_054183887.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X3

  8. XM_054327909.1 → XP_054183884.1  tRNA (uracil-5-)-methyltransferase homolog B isoform X2

RNA

  1. XR_008485507.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96GJ1.1 GenPept UniProtKB/Swiss-Prot:Q96GJ1

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