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TRNT1 Gene(Protein Coding)

TRNA Nucleotidyl Transferase, CCA-Adding, 1

GCID:
GC03P003126
GIFtS:
61
Genes Participants
UDN Logo

Aliases for TRNT1 Gene

Aliases for TRNT1 Gene

  • TRNA Nucleotidyl Transferase, CCA-Adding, 1 2 3 5
  • Mt TRNA CCA-Pyrophosphorylase 3 4
  • Mt TRNA CCA-Diphosphorylase 3 4
  • Mt TRNA Adenylyltransferase 3 4
  • Mt CCA-Adding Enzyme 3 4
  • Mitochondrial TRNA Nucleotidyl Transferase, CCA-Adding 4
  • Mitochondrial CCA-Adding TRNA-Nucleotidyltransferase 3
  • TRNA-Nucleotidyltransferase 1, Mitochondrial 3
  • EC 2.7.7.72 4
  • CGI-47 3
  • MtCCA 3
  • CCA1 3
  • SIFD 3

External Ids for TRNT1 Gene

Previous GeneCards Identifiers for TRNT1 Gene

  • GC03P003097
  • GC03P003143
  • GC03P003168
  • GC03P003102

Summaries for TRNT1 Gene

Entrez Gene Summary for TRNT1 Gene

  • The protein encoded by this gene is a CCA-adding enzyme which belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. This essential enzyme functions by catalyzing the addition of the conserved nucleotide triplet CCA to the 3' terminus of tRNA molecules. Mutations in this gene result in sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

GeneCards Summary for TRNT1 Gene

TRNT1 (TRNA Nucleotidyl Transferase, CCA-Adding, 1) is a Protein Coding gene. Diseases associated with TRNT1 include Sideroblastic Anemia With B-Cell Immunodeficiency, Periodic Fevers, And Developmental Delay and Sideroblastic Anemia. Among its related pathways are Gene Expression and RNA transport. GO annotations related to this gene include RNA binding and nucleotidyltransferase activity.

UniProtKB/Swiss-Prot for TRNT1 Gene

  • Isoform 1: Adds and repairs the conserved 3-CCA sequence necessary for the attachment of amino acids to the 3 terminus of tRNA molecules, using CTP and ATP as substrates.

  • Isoform 2: Adds 2 C residues (CC-) to the 3 terminus of tRNA molecules instead of a complete CCA end as isoform 1 does (in vitro).

Gene Wiki entry for TRNT1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRNT1 Gene

Genomics for TRNT1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for TRNT1 Gene

Enhancers for TRNT1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around TRNT1 on UCSC Golden Path with GeneCards custom track

Promoters for TRNT1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around TRNT1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the TRNT1 gene promoter:

Genomic Location for TRNT1 Gene

Chromosome:
3
Start:
3,126,916 bp from pter
End:
3,152,503 bp from pter
Size:
25,588 bases
Orientation:
Plus strand

Genomic View for TRNT1 Gene

Genes around TRNT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRNT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRNT1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TRNT1 Gene

Proteins for TRNT1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TRNT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96Q11-TRNT1_HUMAN
    Recommended name:
    CCA tRNA nucleotidyltransferase 1, mitochondrial
    Protein Accession:
    Q96Q11
    Secondary Accessions:
    • A8K2Z6
    • B7WP13
    • C9JKA2
    • Q8ND57
    • Q9BS97
    • Q9Y362

    Protein attributes for TRNT1 Gene

    Size:
    434 amino acids
    Molecular mass:
    50128 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Monomer, and homodimer; disulfide-linked.
    SequenceCaution:
    • Sequence=AAD34042.1; Type=Frameshift; Positions=16; Evidence={ECO:0000305}; Sequence=AAH12537.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TRNT1 Gene

    Alternative splice isoforms for TRNT1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRNT1 Gene

Proteomics data for TRNT1 Gene at MOPED

Protein Expression for TRNT1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TRNT1 Gene

  • Ubiquitination at Lys 291
  • Modification sites at PhosphoSitePlus

Other Protein References for TRNT1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for TRNT1

No data available for DME Specific Peptides for TRNT1 Gene

Domains & Families for TRNT1 Gene

Protein Domains for TRNT1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TRNT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96Q11

UniProtKB/Swiss-Prot:

TRNT1_HUMAN :
  • Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family.
Family:
  • Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family.
genes like me logo Genes that share domains with TRNT1: view

No data available for Gene Families for TRNT1 Gene

Function for TRNT1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for TRNT1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
A tRNA precursor + 2 CTP + ATP = a tRNA with a 3 CCA end + 3 diphosphate.
UniProtKB/Swiss-Prot Function:
Isoform 1: Adds and repairs the conserved 3-CCA sequence necessary for the attachment of amino acids to the 3 terminus of tRNA molecules, using CTP and ATP as substrates.
UniProtKB/Swiss-Prot Function:
Isoform 2: Adds 2 C residues (CC-) to the 3 terminus of tRNA molecules instead of a complete CCA end as isoform 1 does (in vitro).

Enzyme Numbers (IUBMB) for TRNT1 Gene

Gene Ontology (GO) - Molecular Function for TRNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004810 tRNA adenylyltransferase activity IDA 11504732
GO:0052927 CTP:tRNA cytidylyltransferase activity IEA --
GO:0052929 ATP:3-cytidine-cytidine-tRNA adenylyltransferase activity IEA --
genes like me logo Genes that share ontologies with TRNT1: view

Phenotypes for TRNT1 Gene

GenomeRNAi human phenotypes for TRNT1:
genes like me logo Genes that share phenotypes with TRNT1: view

Human Phenotype Ontology for TRNT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for TRNT1 Gene

miRTarBase miRNAs that target TRNT1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for TRNT1 Gene

Localization for TRNT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRNT1 Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TRNT1 Gene COMPARTMENTS Subcellular localization image for TRNT1 gene
Compartment Confidence
mitochondrion 5
nucleus 4
cytosol 2
chloroplast 1

Gene Ontology (GO) - Cellular Components for TRNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with TRNT1: view

Pathways & Interactions for TRNT1 Gene

genes like me logo Genes that share pathways with TRNT1: view

Pathways by source for TRNT1 Gene

1 KEGG pathway for TRNT1 Gene

Interacting Proteins for TRNT1 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000251607%0d%0a9606.ENSP00000262415%0d%0a9606.ENSP00000250101%0d%0a9606.ENSP00000344818%0d%0a9606.ENSP00000216392%0d%0a9606.ENSP00000355560%0d%0a
Selected Interacting proteins: ENSP00000251607 for TRNT1 Gene via STRING

Gene Ontology (GO) - Biological Process for TRNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001680 tRNA 3-terminal CCA addition IDA 25193871
GO:0008033 tRNA processing TAS --
genes like me logo Genes that share ontologies with TRNT1: view

No data available for SIGNOR curated interactions for TRNT1 Gene

Drugs & Compounds for TRNT1 Gene

Products:

  1. Drug

(4) Drugs for TRNT1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine triphosphate Approved Nutra 0
Cytidine triphosphate Experimental Pharma 0
Diphosphate Experimental Pharma 0
Magnesium Nutra 0
genes like me logo Genes that share compounds with TRNT1: view

Transcripts for TRNT1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for TRNT1 Gene

(7) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(132) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TRNT1 Gene

TRNA nucleotidyl transferase, CCA-adding, 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRNT1 Gene

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

Relevant External Links for TRNT1 Gene

GeneLoc Exon Structure for
TRNT1
ECgene alternative splicing isoforms for
TRNT1

Expression for TRNT1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for TRNT1 Gene

mRNA expression in normal human tissues for TRNT1 Gene
mRNA expression by BioGPS for TRNT1 GenemRNA expression by GTEx for TRNT1 Gene

Protein differential expression in normal tissues from HIPED for TRNT1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.7) and Lymph node (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for TRNT1 Gene



SOURCE GeneReport for Unigene cluster for TRNT1 Gene Hs.732725

genes like me logo Genes that share expression patterns with TRNT1: view

Protein tissue co-expression partners for TRNT1 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for TRNT1 Gene

Orthologs for TRNT1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TRNT1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia TRNT1 35
  • 87.71 (n)
  • 91.01 (a)
TRNT1 36
  • 91 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia TRNT1 35
  • 91.17 (n)
  • 92.17 (a)
TRNT1 36
  • 92 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Trnt1 35
  • 87.94 (n)
  • 92.86 (a)
Trnt1 16
Trnt1 36
  • 93 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia TRNT1 35
  • 99.62 (n)
  • 99.54 (a)
TRNT1 36
  • 99 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Trnt1 35
  • 88.1 (n)
  • 92.4 (a)
oppossum
(Monodelphis domestica)
 Mammalia TRNT1 36
  • 82 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia TRNT1 36
  • 75 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves TRNT1 35
  • 74.85 (n)
  • 74.94 (a)
TRNT1 36
  • 75 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia TRNT1 36
  • 74 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia trnt1 35
  • 65.17 (n)
  • 66.92 (a)
African clawed frog
(Xenopus laevis)
 Amphibia LOC398421 35
zebrafish
(Danio rerio)
 Actinopterygii trnt1 35
  • 65.1 (n)
  • 70.86 (a)
trnt1 36
  • 67 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta CG2100 37
  • 49 (a)
CG2100 35
  • 51.98 (n)
  • 50.89 (a)
CG2100 36
  • 43 (a)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP002600 35
  • 54.91 (n)
  • 51.89 (a)
worm
(Caenorhabditis elegans)
 Secernentea F55B12.4 37
  • 43 (a)
hpo-31 35
  • 53.06 (n)
  • 46.35 (a)
hpo-31 36
  • 42 (a)
 OneToOne
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes CCA1 36
  • 19 (a)
 OneToOne
CCA1 38
sea squirt
(Ciona savignyi)
 Ascidiacea -- 36
  • 44 (a)
 OneToOne
Species with no ortholog for TRNT1:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TRNT1 Gene

ENSEMBL:
Gene Tree for TRNT1 (if available)
TreeFam:
Gene Tree for TRNT1 (if available)

Paralogs for TRNT1 Gene

Pseudogenes.org Pseudogenes for TRNT1 Gene

genes like me logo Genes that share paralogs with TRNT1: view

No data available for Paralogs for TRNT1 Gene

Variants for TRNT1 Gene

Sequence variations from dbSNP and Humsavar for TRNT1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs334773 - 3,129,108(-) GCTTC(A/G)GAAGG nc-transcript-variant, reference, missense
VAR_072421 Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD)
VAR_072422 Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD)
VAR_072423 Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD)
VAR_072424 Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD)

Structural Variations from Database of Genomic Variants (DGV) for TRNT1 Gene

Variant ID Type Subtype PubMed ID
esv2422274 CNV Duplication 17116639
esv2751994 CNV Gain 17911159
nsv521796 CNV Loss 19592680
nsv876405 CNV Gain 21882294
dgv787n67 CNV Loss 20364138
nsv834604 CNV Gain 17160897

Variation tolerance for TRNT1 Gene

Residual Variation Intolerance Score: 28.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.12; 22.68% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TRNT1 Gene

Human Gene Mutation Database (HGMD)
TRNT1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRNT1 Gene

Disorders for TRNT1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for TRNT1 Gene - From: OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search TRNT1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TRNT1_HUMAN
  • Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) [MIM:616084]: An autosomal recessive disease characterized by severe sideroblastic anemia with onset in the neonatal period or infancy, recurrent periodic fevers without an infectious etiology, B-cell lymphopenia and hypogammaglobulinemia. Affected individuals show delayed psychomotor development with variable neurodegeneration. Additional variable features include sensorineural hearing loss, retinitis pigmentosa, nephrocalcinosis, and cardiomyopathy. {ECO:0000269 PubMed:25193871}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for TRNT1

Genetic Association Database (GAD)
TRNT1
Human Genome Epidemiology (HuGE) Navigator
TRNT1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TRNT1
genes like me logo Genes that share disorders with TRNT1: view

No data available for Genatlas for TRNT1 Gene

Publications for TRNT1 Gene

  1. Identification and characterization of mammalian mitochondrial tRNA nucleotidyltransferases. (PMID: 11504732) Nagaike T. … Ueda T. (J. Biol. Chem. 2001) 2 3 4 23 67
  2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai C.-H. … Lin W.-C. (Genome Res. 2000) 2 3
  3. On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. (PMID: 25640237) Kuhn C.D. … Joshua-Tor L. (Cell 2015) 3
  4. The 3' addition of CCA to mitochondrial tRNASer(AGY) is specifically impaired in patients with mutations in the tRNA nucleotidyl transferase TRNT1. (PMID: 25652405) Sasarman F. … Shoubridge E.A. (Hum. Mol. Genet. 2015) 3
  5. Domain movements during CCA-addition: a new function for motif C in the catalytic core of the human tRNA nucleotidyltransferases. (PMID: 25849199) Ernst F.G. … MAPrl M. (RNA Biol 2015) 3

Products for TRNT1 Gene

Sources for TRNT1 Gene

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