TRMT2B Gene
protein-coding GIFtS: 46
GCID: GC0XM100264
|
|
tRNA methyltransferase 2 homolog B (S. cerevisiae)(Previous name: chromosome X open reading frame 34 )
(Previous symbol: CXorf34)
| |
Aliases
for TRMT2B gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| TRNA Methyltransferase 2 Homolog B (S. Cerevisiae)1 2 | | Chromosome X Open Reading Frame 341 | | CXorf341 2 3 | | DJ341D10.31 | | TRM2 Homolog2 3 | | TRM2 TRNA Methyltransferase 2 Homolog B2 | | EC 2.1.1.353 8 | | TRNA (Uracil(54)-C(5))-Methyltransferase Homolog2 | | FLJ126871 | | TRNA (Uracil-5-)-Methyltransferase Homolog2 |
Export aliases for TRMT2B gene to outside databasesPrevious GC identifers: GC0XM100150 GC0XM090068 |
Summaries
for TRMT2B gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for TRMT2B:
This gene encodes a homolog of the TRM2 gene in S. cerevisiae. The yeast gene encodes a tRNA methyltransferase thatplays a role in tRNA maturation. The yeast protein also has endo-exonuclease activity and may be involved in DNAdouble strand break repair. Alternative splicing results in multiple transcripts encoding different isoforms.(provided by RefSeq, Nov 2009)
UniProtKB/Swiss-Prot: TRM2_HUMAN, Q96GJ1Function: Probable S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridineat position 54 (m5U54) in all tRNA. May also have a role in tRNA stabilization or maturation (By similarity)
|
Genomic Views
for TRMT2B gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000023.10 NC_018934.1 NT_011651.17
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the TRMT2B gene promoter:
HOXA9 HOXA9B RFX1 Brachyury Gfi-1 POU2F1 POU2F1a HOXA5 Meis-1a Meis-1
Other transcription factors
Search SABiosciences Chromatin IP Primers for TRMT2B
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TRMT2B |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: Xq22.1 Ensembl cytogenetic band: Xq22.1 HGNC cytogenetic band: Xq22.1TRMT2B Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome X GeneLoc Exon Structure GeneLoc location for GC0XM100264: view genomic region
(about GC identifiers)
Start:
|
100,264,334 bp from pter |
End:
|
100,307,105 bp from pter |
Size:
|
42,772 bases |
Orientation:
|
minus strand |
|
Proteins
for TRMT2B gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: TRM2_HUMAN, Q96GJ1 (See
protein sequence)Recommended Name: tRNA (uracil(54)-C(5))-methyltransferase homolog Size: 504 amino acids; 56476 Da
Secondary accessions: A6NDG5 A6NEI9 A6NMG6 Q5JPF0 Q5JVY6 Q96HU7 Q96IH9 Q9H9K2Alternative splicing: 3 isoforms: Q96GJ1-1 Q96GJ1-2 Q96GJ1-3 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for TRMT2B: NX_Q96GJ1
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q96GJ1
2 DME Specific Peptides for TRMT2B (Q96GJ1)
TRMT2B Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (4 alternative transcripts):
NP_001161442.1 NP_001161443.1 NP_001161444.1 NP_079193.2
ENSEMBL proteins: ENSP00000437279 ENSP00000362030 ENSP00000362026 ENSP00000362027 ENSP00000340970 ENSP00000438134 ENSP00000362022
Human Recombinant Protein Products:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005739 | mitochondrion |
IEA | -- |
TRMT2B for ontologies About GeneDecksing
TRMT2B Antibody Products:
Assay Products for TRMT2B: |
Protein
Domains /
Families
for TRMT2B gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
TRMT2B for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q96GJ1ProtoNet protein and cluster: Q96GJ1 UniProtKB/Swiss-Prot: TRM2_HUMAN, Q96GJ1Similarity: Belongs to the methyltransferase superfamily. RNA M5U methyltransferase family |
Function
for TRMT2B gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: TRM2_HUMAN, Q96GJ1Function: Probable S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridineat position 54 (m5U54) in all tRNA. May also have a role in tRNA stabilization or maturation (By similarity)Catalytic activity: S-adenosyl-L-methionine + uridine(54) in tRNA = S-adenosyl-L-homocysteine + 5-methyluridine(54) intRNAEnzyme Number (IUBMB): EC 2.1.1.351 2
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TRMT2B (see all 5)
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRMT2B |
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0030697 | S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity |
IEA | -- |
TRMT2B for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for TRMT2B:
|
Pathways & Interactions
for TRMT2B gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TRMT2B
|
Drugs & Compounds
for TRMT2B gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for TRMT2B
1 HMDB Compound for TRMT2B About this table
Search CenterWatch for drugs/clinical trials and news about TRMT2B / TRM2
|
Transcripts
for TRMT2B gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for TRMT2B gene (4 alternative transcripts): NM_001167970.1 NM_001167971.1 NM_001167972.1 NM_024917.5 Unigene Cluster for TRMT2B: TRNA methyltransferase 2 homolog B (S. cerevisiae) Hs.496501 [show with all ESTs]Unigene Representative Sequence: NM_0249179 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000490509 ENST00000372939 ENST00000372935 ENST00000372936 ENST00000478422
ENST00000488615 ENST00000338687(uc004egr.3 uc004egv.3) ENST00000545398(uc004egt.3 uc004egq.3 uc004egs.3 uc004egu.3)
ENST00000372931
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for TRMT2B (see all 7)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TRMT2B (see all 5)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
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Additional cDNA sequence: AK022749.1 AK315780.1 AL832849.1 BC008067.2 BC009437.1 BC020116.1 BC034272.2 BX647969.1 16 DOTS entries: DT.95126701 DT.101984366 DT.70104983 DT.91765842 DT.121281428 DT.91765841 DT.95310537 DT.95126689 DT.100027702 DT.100789397 DT.100789400 DT.121281433 DT.91765849 DT.95362513 DT.92349294 DT.95144903 24/130 AceView cDNA sequences (see all 130): BG473171 BQ919445 BQ063167 BE734445 BQ055470 AL556799 BE409102 W39709 BQ952071 BQ643429 BG481630 BQ059395 BG390275 CR605503 BQ423218 BQ052955 BE258334 BQ429000 BE253147 BI333489 BX091538 BQ066438 BC007526 AI765573
GeneLoc Exon Structure
5/24 Alternative Splicing Database (ASD) splice patterns (SP) for TRMT2B (see all 24) About this scheme
| ExUns: | 1a | · | 1b | · | 1c | · | 1d | · | 1e | · | 1f | · | 1g | ^ | 2 | ^ | 3a | · | 3b | · | 3c | ^ | 4 | ^ | 5a | · | 5b | ^ | 6a | · | 6b | ^ | 7a | · | 7b | ^ | 8a | · | 8b | · | 8c | · | 8d | · | 8e | ^ | 9a | · | 9b | · | 9c | ^ |
|---|
|
| SP1: | | | | | | | | | | | | | - | | - | | - | | - | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | | | - | | | | - | | - | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | - | | | | - | | - | | - | | - | | - | | - | | | | | | - | | - | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | - | | - | | - | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| ExUns: | 10a | · | 10b | · | 10c | ^ | 11 | ^ | 12a | · | 12b | ^ | 13 | ^ | 14 | ^ | 15 | ^ | 16 | ^ | 17a | · | 17b |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | | | - | | | | | | |
| SP3: | | | | | | | | | | | | | | | | | | | - | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for TRMT2B
|
Expression
for TRMT2B gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| TRMT2B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AAGTGAATAC
About this image
See TRMT2B Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for TRMT2B
SOURCE GeneReport for Unigene cluster: Hs.496501
SABiosciences Custom PCR Arrays for TRMT2B
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for TRMT2B
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRMT2B |
Orthologs
for TRMT2B gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the last universal common ancestor (LUCA).
Orthologs for TRMT2B gene from 8/25 species (see all 25) About this table
ENSEMBL Gene Tree for TRMT2B (if available)
TreeFam Gene Tree for TRMT2B (if available) |
Paralogs
for TRMT2B gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for TRMT2B gene
- TRMT2A2
2 SIMAP similar genes for TRMT2B using alignment to 2 protein entries: TRM2_HUMAN (see all proteins):TUBA1C TRMT2A
TRMT2B for paralogs About GeneDecksing
1 Pseudogenes.org Pseudogene for TRMT2B
PGOHUM00000245120
|
Genomic Variants
for TRMT2B gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr X pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for TRMT2B (100264334 - 100307105 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for TRMT2B
1 CNV: 52901
Locus Specific Mutation Databases (LSDB): TRMT2B
| SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TRMT2B |
|
Disorders
/ Diseases
for TRMT2B gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
TRMT2B for disorders About GeneDecksing
3  diseases for TRMT2B: About MalaCardshomocysteine pneumonia malaria
Export disorders for TRMT2B gene to outside databases
|
Publications
for TRMT2B gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for TRMT2B gene integrated from 9 sources:
(articles sorted by number of sources associating them with TRMT2B) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2, 3 Ota T.... Sugano S. (2004)
- Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
- The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
- Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
- The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (2005)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
- Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
|
External Searches for TRMT2B gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing TRMT2B gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing TRMT2B gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing TRMT2B gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for TRMT2B | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for TRMT2B gene:
Search GeneIP for patents involving TRMT2B
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for TRMT2B gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat TRMT2B | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TRMT2B | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TRMT2B | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat TRMT2B | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat TRMT2B | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat TRMT2B |
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 | | | TRMT2B Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRMT2B |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TRMT2B |
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