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Aliases for TRMT13 Gene

Aliases for TRMT13 Gene

  • TRNA Methyltransferase 13 Homolog 2 3
  • TRNA Methyltransferase 13 Homolog (S. Cerevisiae) 2 5
  • Coiled-Coil Domain-Containing Protein 76 3 4
  • Coiled-Coil Domain Containing 76 2 3
  • CCDC76 3 4
  • TRNA Guanosine-2-O-Methyltransferase TRM13 Homolog 3
  • TRNA [Gm4] Methyltransferase 3
  • EC 2.1.1.225 4

External Ids for TRMT13 Gene

Previous HGNC Symbols for TRMT13 Gene

  • CCDC76

Previous GeneCards Identifiers for TRMT13 Gene

  • GC01P100599

Summaries for TRMT13 Gene

GeneCards Summary for TRMT13 Gene

TRMT13 (TRNA Methyltransferase 13 Homolog) is a Protein Coding gene. Among its related pathways are Gene Expression and tRNA processing. GO annotations related to this gene include methyltransferase activity and tRNA methyltransferase activity.

UniProtKB/Swiss-Prot for TRMT13 Gene

  • tRNA methylase which 2-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRMT13 Gene

Genomics for TRMT13 Gene

Regulatory Elements for TRMT13 Gene

Promoters for TRMT13 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around TRMT13 on UCSC Golden Path with GeneCards custom track

Genomic Location for TRMT13 Gene

Chromosome:
1
Start:
100,133,147 bp from pter
End:
100,150,498 bp from pter
Size:
17,352 bases
Orientation:
Plus strand

Genomic View for TRMT13 Gene

Genes around TRMT13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRMT13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRMT13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRMT13 Gene

Proteins for TRMT13 Gene

  • Protein details for TRMT13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUP7-TRM13_HUMAN
    Recommended name:
    tRNA:m(4)X modification enzyme TRM13 homolog
    Protein Accession:
    Q9NUP7
    Secondary Accessions:
    • Q5VVL0
    • Q9NW65

    Protein attributes for TRMT13 Gene

    Size:
    481 amino acids
    Molecular mass:
    54247 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for TRMT13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRMT13 Gene

Proteomics data for TRMT13 Gene at MOPED

Post-translational modifications for TRMT13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TRMT13 Gene

No data available for DME Specific Peptides for TRMT13 Gene

Domains & Families for TRMT13 Gene

Protein Domains for TRMT13 Gene

Suggested Antigen Peptide Sequences for TRMT13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NUP7

UniProtKB/Swiss-Prot:

TRM13_HUMAN :
  • Belongs to the TRM13 family.
  • Contains 1 CHHC-type zinc finger.
Family:
  • Belongs to the TRM13 family.
Similarity:
  • Contains 1 CHHC-type zinc finger.
genes like me logo Genes that share domains with TRMT13: view

No data available for Gene Families for TRMT13 Gene

Function for TRMT13 Gene

Molecular function for TRMT13 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2-O-methyluridine.
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + cytidine(4) in tRNA(Pro) = S-adenosyl-L-homocysteine + 2-O-methylcytidine(4) in tRNA(Pro).
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + cytidine(4) in tRNA(Gly)(GCC) = S-adenosyl-L-homocysteine + 2-O-methylcytidine(4) in tRNA(Gly)(GCC).
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + adenosine(4) in tRNA(His) = S-adenosyl-L-homocysteine + 2-O-methyladenosine(4) in tRNA(His).
UniProtKB/Swiss-Prot Function:
tRNA methylase which 2-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His).

Enzyme Numbers (IUBMB) for TRMT13 Gene

Gene Ontology (GO) - Molecular Function for TRMT13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
genes like me logo Genes that share ontologies with TRMT13: view
genes like me logo Genes that share phenotypes with TRMT13: view

Animal Model Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TRMT13 Gene

Localization for TRMT13 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TRMT13 Gene COMPARTMENTS Subcellular localization image for TRMT13 gene
Compartment Confidence
cytosol 3
nucleus 3

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for TRMT13 Gene

Pathways & Interactions for TRMT13 Gene

genes like me logo Genes that share pathways with TRMT13: view

Pathways by source for TRMT13 Gene

Interacting Proteins for TRMT13 Gene

STRING Interaction Network Preview (showing 3 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000359160%0d%0a9606.ENSP00000385269%0d%0a9606.ENSP00000310226%0d%0a9606.ENSP00000387286%0d%0a
Selected Interacting proteins: ENSP00000359160 for TRMT13 Gene via STRING

Gene Ontology (GO) - Biological Process for TRMT13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030488 tRNA methylation IBA --
genes like me logo Genes that share ontologies with TRMT13: view

No data available for SIGNOR curated interactions for TRMT13 Gene

Drugs & Compounds for TRMT13 Gene

(2) Drugs for TRMT13 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 0
genes like me logo Genes that share compounds with TRMT13: view

Transcripts for TRMT13 Gene

Unigene Clusters for TRMT13 Gene

TRNA methyltransferase 13 homolog (S. cerevisiae):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for TRMT13 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11 ^ 12
SP1: -
SP2: - -
SP3: - - - -
SP4: -
SP5: - -
SP6: - -
SP7: -
SP8:
SP9:

Relevant External Links for TRMT13 Gene

GeneLoc Exon Structure for
TRMT13
ECgene alternative splicing isoforms for
TRMT13

Expression for TRMT13 Gene

mRNA expression in normal human tissues for TRMT13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRMT13 Gene

This gene is overexpressed in Urinary Bladder (14.9), Liver (13.7), Prostate (9.6), Lung (8.8), and Rectum (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for TRMT13 Gene



SOURCE GeneReport for Unigene cluster for TRMT13 Gene Hs.729095

genes like me logo Genes that share expression patterns with TRMT13: view

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for TRMT13 Gene

Orthologs for TRMT13 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRMT13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRMT13 35
  • 99.72 (n)
  • 99.38 (a)
CCDC76 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CCDC76 36
  • 91 (a)
OneToOne
CCDC76 35
  • 92.45 (n)
  • 90.64 (a)
dog
(Canis familiaris)
Mammalia TRMT13 36
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Trmt13 36
  • 85 (a)
OneToOne
Trmt13 35
  • 86.88 (n)
  • 86.53 (a)
Trmt13 16
oppossum
(Monodelphis domestica)
Mammalia TRMT13 36
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRMT13 36
  • 74 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Trmt13 35
  • 88.49 (n)
  • 86.32 (a)
chicken
(Gallus gallus)
Aves TRMT13 36
  • 62 (a)
OneToOne
TRMT13 35
  • 68.67 (n)
  • 65.74 (a)
lizard
(Anolis carolinensis)
Reptilia TRMT13 36
  • 63 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.31050 35
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.18070 35
trmt13 35
  • 61.82 (n)
  • 60.28 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9602 35
zebrafish
(Danio rerio)
Actinopterygii trmt13 35
  • 63.01 (n)
  • 61.42 (a)
trmt13 36
  • 57 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000681 35
  • 45.71 (n)
  • 40.26 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG18048 35
  • 46.65 (n)
  • 36.93 (a)
CG18048 36
  • 32 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y49A3A.3 36
  • 29 (a)
OneToOne
Y49A3A.3 35
  • 46.15 (n)
  • 33.24 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL163W 35
  • 40.27 (n)
  • 34.13 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM13 35
  • 49.43 (n)
  • 38.64 (a)
TRM13 36
  • 29 (a)
OneToOne
TRM13 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E07547g 35
  • 46.01 (n)
  • 36.46 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G01880 35
  • 48.19 (n)
  • 38.54 (a)
rice
(Oryza sativa)
Liliopsida Os03g0833200 35
  • 44.34 (n)
  • 32.55 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trm13 35
  • 49.26 (n)
  • 38.87 (a)
Species with no ortholog for TRMT13:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TRMT13 Gene

ENSEMBL:
Gene Tree for TRMT13 (if available)
TreeFam:
Gene Tree for TRMT13 (if available)

Paralogs for TRMT13 Gene

No data available for Paralogs for TRMT13 Gene

Variants for TRMT13 Gene

Sequence variations from dbSNP and Humsavar for TRMT13 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
VAR_057806 -
rs561119 -- 100,138,335(-) ACTTA(C/T)GTTGT intron-variant
rs2784175 -- 100,137,335(+) GGACT(A/G)TAGGC intron-variant
rs6681721 -- 100,144,083(+) CTGTG(C/T)TAAGA nc-transcript-variant, reference, synonymous-codon
rs7553958 -- 100,146,727(+) tctcc(A/C)tctcc intron-variant

Variation tolerance for TRMT13 Gene

Residual Variation Intolerance Score: 17.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.67; 14.25% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TRMT13 Gene

HapMap Linkage Disequilibrium report
TRMT13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for TRMT13 Gene

Disorders for TRMT13 Gene

Relevant External Links for TRMT13

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TRMT13

No disorders were found for TRMT13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TRMT13 Gene

Publications for TRMT13 Gene

  1. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 67
  2. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. (PMID: 11799066) Weinmann A.S. … Farnham P.J. (Genes Dev. 2002) 2 3
  3. Ubiquitin-mediated proteolysis of HuR by heat shock. (PMID: 19322201) Abdelmohsen K. … Gorospe M. (EMBO J. 2009) 3
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3

Products for TRMT13 Gene

Sources for TRMT13 Gene

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