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Aliases for TRMT13 Gene

Aliases for TRMT13 Gene

  • TRNA Methyltransferase 13 Homolog 2 3 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 Methyltransferase 13 Homolog (S. Cerevisiae) 2
  • TRNA:M(4)X Modification Enzyme 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. Gene Ontology (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).

Additional gene information for TRMT13 Gene

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

Genomics for TRMT13 Gene

GeneHancer (GH) Regulatory Elements for TRMT13 Gene

Promoters and enhancers for TRMT13 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I100130 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 564.4 -1.0 -1038 4.2 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 GLIS1 NBN TRMT13 SASS6 SLC30A7 HNRNPA1P68 ENSG00000235795 EXTL2 RTCA MFSD14A BRI3P1 SLC35A3
GH01I100348 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 42.9 +219.1 219086 7.1 FEZF1 DMAP1 YBX1 YY1 ZNF213 ZNF143 ZNF263 SP3 NFYC MEF2D CDC14A MFSD14A SLC30A7 BRI3P1 TRMT13 SASS6 HNRNPA1P68 ENSG00000235795 RTCA VCAM1
GH01I101024 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 23.5 +892.9 892909 4 HDGF SMAD1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 DPH5 GC01M100998 LOC102606465 HNRNPA1P68 TRMT13 SLC30A7 ENSG00000235795 MFSD14A BRI3P1 SASS6
GH01I099644 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 13.7 -485.1 -485064 7.2 HDGF PKNOX1 ATF1 FOXA2 ARID4B FEZF1 ZNF48 YY1 RUNX3 RXRA PALMD TRMT13 ENSG00000227034 MFSD14A BRI3P1 RTCA AGL GC01P099667
GH01I100036 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 14.7 -94.4 -94420 4.1 SMAD1 ARNT MLX ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 MFSD14A SASS6 LRRC39 TRMT13 SLC30A7 BRI3P1 RTCA AGL ENSG00000241073 ENSG00000283761
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TRMT13 on UCSC Golden Path with GeneCards custom track

Genomic Locations for TRMT13 Gene

Genomic Locations for TRMT13 Gene
chr1:100,133,147-100,150,498
(GRCh38/hg38)
Size:
17,352 bases
Orientation:
Plus strand
chr1:100,598,706-100,616,054
(GRCh37/hg19)

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

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

Gene Families for TRMT13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

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 methyltransferase TRM13 family.
Family:
  • Belongs to the methyltransferase TRM13 family.
genes like me logo Genes that share domains with TRMT13: view

Function for TRMT13 Gene

Molecular function for TRMT13 Gene

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 --
GO:0008175 tRNA methyltransferase activity IBA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding 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

CRISPR Products

Inhibitory RNA Products

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

Localization for TRMT13 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRMT13 gene
Compartment Confidence
nucleus 3
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

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

Gene Ontology (GO) - Biological Process for TRMT13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030488 tRNA methylation IBA --
GO:0032259 methylation IEA --
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

(1) Drugs for TRMT13 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for TRMT13 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0
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:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for TRMT13 Gene



NURSA nuclear receptor signaling pathways regulating expression of TRMT13 Gene:

TRMT13

SOURCE GeneReport for Unigene cluster for TRMT13 Gene:

Hs.729095
genes like me logo Genes that share expression patterns with TRMT13: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33
  • 99.72 (n)
CCDC76 34
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CCDC76 34 33
  • 92.45 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TRMT13 34
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Trmt13 33
  • 88.49 (n)
mouse
(Mus musculus)
Mammalia Trmt13 33 16 34
  • 86.88 (n)
oppossum
(Monodelphis domestica)
Mammalia TRMT13 34
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRMT13 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves TRMT13 33 34
  • 68.67 (n)
lizard
(Anolis carolinensis)
Reptilia TRMT13 34
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia trmt13 33
  • 61.82 (n)
Str.18070 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.31050 33
zebrafish
(Danio rerio)
Actinopterygii trmt13 33 34
  • 63.01 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9602 33
fruit fly
(Drosophila melanogaster)
Insecta CG18048 33 34
  • 46.65 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000681 33
  • 45.71 (n)
worm
(Caenorhabditis elegans)
Secernentea Y49A3A.3 33 34
  • 46.15 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM13 33 34 36
  • 49.43 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E07547g 33
  • 46.01 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL163W 33
  • 40.27 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G01880 33
  • 48.19 (n)
rice
(Oryza sativa)
Liliopsida Os03g0833200 33
  • 44.34 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trm13 33
  • 49.26 (n)
Species where no ortholog for TRMT13 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1000091392 -- 100,150,171(+) A/G 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000179209 -- 100,139,129(+) G/A intron_variant
rs1000278459 -- 100,133,107(+) G/C 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000491855 -- 100,138,485(+) A/T intron_variant
rs1000523331 -- 100,149,219(+) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for TRMT13 Gene

Variant ID Type Subtype PubMed ID
esv275107 CNV loss 21479260
nsv2121 CNV insertion 18451855
nsv830804 CNV gain 17160897

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)

Additional Variant Information for TRMT13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRMT13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRMT13 Gene

Disorders for TRMT13 Gene

Additional Disease Information for 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 SG … Prigmore E (Nature 2006) 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. (PMID: 11799066) Weinmann AS … Farnham PJ (Genes & development 2002) 2 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for TRMT13 Gene

Sources for TRMT13 Gene

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