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

    Gene ID: 79979, updated on 27-Nov-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 MIM:301128; 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_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (100973366..101052111, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (99416819..99495549, complement)
    RS_2024_09 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 ARF 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. Association of TRMT2B gene variants with juvenile amyotrophic lateral sclerosis. Liu Y, et al. Front Med, 2024 Feb. PMID 37874476
    3. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Dai W, et al. Nat Chem Biol, 2021 Nov. PMID 34556860, Free PMC Article
    4. APEX Fingerprinting Reveals the Subcellular Localization of Proteins of Interest. Lee SY, et al. Cell Rep, 2016 May 24. PMID 27184847
    5. 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

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association of TRMT2B gene variants with juvenile amyotrophic lateral sclerosis.
      Title: Association of TRMT2B gene variants with juvenile amyotrophic lateral sclerosis.
    2. 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)

    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 
    located_in mitochondrion HTP 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_2024_08

    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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