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Aliases for TRNT1 Gene

Aliases for TRNT1 Gene

  • TRNA Nucleotidyl Transferase 1 2 3 5
  • TRNA Nucleotidyl Transferase, CCA-Adding, 1 2 3
  • ATP(CTP):TRNA Nucleotidyltransferase 2 3
  • TRNA CCA Nucleotidyl Transferase 1 2 3
  • Mt TRNA CCA-Pyrophosphorylase 3 4
  • Mt TRNA CCA-Diphosphorylase 3 4
  • Mt TRNA Adenylyltransferase 3 4
  • Mt CCA-Adding Enzyme 3 4
  • CCA-Adding Enzyme 2 3
  • Mitochondrial TRNA Nucleotidyl Transferase, CCA-Adding 4
  • Mitochondrial CCA-Adding TRNA-Nucleotidyltransferase 3
  • CCA TRNA Nucleotidyltransferase 1, Mitochondrial 3
  • TRNA-Nucleotidyltransferase 1, Mitochondrial 3
  • EC 2.7.7.72 4
  • CGI-47 3
  • MtCCA 3
  • CCA1 3
  • RPEM 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 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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRNT1 Gene

Genomics for TRNT1 Gene

Regulatory Elements for TRNT1 Gene

Enhancers for TRNT1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G003170 1.2 Ensembl ENCODE dbSUPER 29.6 +46.6 46625 6.2 CTCF ZNF654 IRF2 RAD21 GATA3 ZNF316 GATA2 HNF4G HNF4A ZBTB33 TRNT1 CRBN IL5RA ENSG00000271870
GH03G003145 0.9 dbSUPER 34.5 +20.3 20293 3.4 ATF1 PKNOX1 ARNT ZNF766 GATA2 PAF1 USF2 REST ZNF592 MEF2D TRNT1 CRBN IL5RA ENSG00000253049 ENSG00000271870 GC03P003130
GH03G003177 1.4 ENCODE dbSUPER 18.4 +52.1 52061 2.7 FOXA2 MLX ARNT AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 CRBN TRNT1 ENSG00000271870
GH03G003136 1.1 dbSUPER 21.5 +11.8 11782 3.9 HNRNPUL1 FOXA2 MLX AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 CRBN TRNT1 ENSG00000253049 ENSG00000271870 GC03P003130
GH03G003149 0.9 dbSUPER 22.3 +24.4 24399 4.4 HDAC1 ATF1 FOXA2 TBL1XR1 NFRKB TCF12 GATA2 BCLAF1 CREM PAF1 TRNT1 CRBN ENSG00000253049 ENSG00000271870 GC03P003130
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000147817 184 1401 HNRNPUL1 CREB3L1 ARNT AGO1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

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 StructureGene Density

RefSeq DNA sequence for TRNT1 Gene

Proteins for TRNT1 Gene

  • 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

Post-translational modifications for TRNT1 Gene

  • Ubiquitination at Lys291
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for TRNT1
  • Santa Cruz Biotechnology (SCBT) Antibodies for TRNT1

No data available for DME Specific Peptides for TRNT1 Gene

Domains & Families for TRNT1 Gene

Protein Domains for TRNT1 Gene

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

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:0000049 tRNA binding IDA 11504732
GO:0000166 nucleotide binding IEA --
GO:0003723 RNA binding IEA --
GO:0004810 tRNA adenylyltransferase activity IDA 11504732
GO:0005524 ATP binding TAS 11504732
genes like me logo Genes that share ontologies with TRNT1: view
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 Models for TRNT1 Gene

MGI Knock Outs for TRNT1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for 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
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 TRNT1 gene
Compartment Confidence
mitochondrion 5
nucleus 4
cytosol 2

Gene Ontology (GO) - Cellular Components for TRNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IDA --
GO:0005654 nucleoplasm TAS --
GO:0005739 mitochondrion IEA,IDA 11504732
GO:0005759 mitochondrial matrix 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

Gene Ontology (GO) - Biological Process for TRNT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001680 tRNA 3-terminal CCA addition IEA,IDA 25193871
GO:0006396 RNA processing IEA --
GO:0006626 protein targeting to mitochondrion TAS 11504732
GO:0008033 tRNA processing IEA --
GO:0042780 tRNA 3-end 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

(3) 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
Magnesium Nutra 0

(1) Additional Compounds for TRNT1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with TRNT1: view

Transcripts for TRNT1 Gene

Unigene Clusters for TRNT1 Gene

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

CRISPR Products

Inhibitory RNA Products

Clone 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

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for TRNT1 Gene



Protein tissue co-expression partners for TRNT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TRNT1 Gene:

TRNT1

SOURCE GeneReport for Unigene cluster for TRNT1 Gene:

Hs.732725

Evidence on tissue expression from TISSUES for TRNT1 Gene

  • Nervous system(4.6)
  • Blood(4.2)
  • Bone marrow(4.1)
  • Lung(3.1)
  • Intestine(2.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TRNT1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • nervous
  • skeletal muscle
Organs:
General:
  • blood
  • bone marrow
  • red blood cell
  • white blood cell
genes like me logo Genes that share expression patterns with TRNT1: view

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
chimpanzee
(Pan troglodytes)
Mammalia TRNT1 34 35
  • 99.62 (n)
dog
(Canis familiaris)
Mammalia TRNT1 34 35
  • 91.17 (n)
rat
(Rattus norvegicus)
Mammalia Trnt1 34
  • 88.1 (n)
mouse
(Mus musculus)
Mammalia Trnt1 34 16 35
  • 87.94 (n)
cow
(Bos Taurus)
Mammalia TRNT1 34 35
  • 87.71 (n)
oppossum
(Monodelphis domestica)
Mammalia TRNT1 35
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRNT1 35
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves TRNT1 34 35
  • 74.85 (n)
lizard
(Anolis carolinensis)
Reptilia TRNT1 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia trnt1 34
  • 65.17 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC398421 34
zebrafish
(Danio rerio)
Actinopterygii trnt1 34 35
  • 65.1 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002600 34
  • 54.91 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG2100 36 34 35
  • 51.98 (n)
worm
(Caenorhabditis elegans)
Secernentea hpo-31 34 35
  • 53.06 (n)
F55B12.4 36
  • 43 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CCA1 35 37
  • 19 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 44 (a)
OneToOne
Species where no ortholog for TRNT1 was found in the sources mined by GeneCards:
  • 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
rs199931785 Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) [MIM:616084] 3,148,095(+) AGTGG(A/G)AAAAA nc-transcript-variant, downstream-variant-500B, reference, missense
rs370011798 Pathogenic, Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) [MIM:616084] 3,146,489(+) AGCAA(C/T)TGCAG nc-transcript-variant, reference, missense
rs606231287 Pathogenic, Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) [MIM:616084] 3,144,671(+) ACAGA(G/T)AATAC nc-transcript-variant, reference, missense
rs606231289 Pathogenic, Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) [MIM:616084] 3,144,599(+) CACTT(C/T)ATTTG nc-transcript-variant, reference, missense
rs606231290 Pathogenic, Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) [MIM:616084] 3,140,628(+) TCTCA(C/T)TATAA nc-transcript-variant, reference, missense

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

Variant ID Type Subtype PubMed ID
dgv4636n100 CNV gain 25217958
dgv787n67 CNV loss 20364138
esv2422274 CNV duplication 17116639
esv2751994 CNV gain 17911159
esv3595052 CNV loss 21293372
nsv521796 CNV loss 19592680
nsv589371 CNV loss 21841781
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
SNPedia medical, phenotypic, and genealogical associations of SNPs for
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, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
sideroblastic anemia with b-cell immunodeficiency, periodic fevers, and developmental delay
  • sideroblastic anemia with b-cell immunodeficiency, periodic fevers and developmental delay
sideroblastic anemia
  • anemia sideroblastic
cataract 7
  • cca1
retinitis pigmentosa
  • retinitis pigmentosa 1
autosomal recessive disease
  • autosomal recessive disorder
- 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
  • Retinitis pigmentosa and erythrocytic microcytosis (RPEM) [MIM:616959]: An autosomal recessive disease characterized by retinitis pigmentosa, red blood cell microcytosis and anisocytosis with mild anemia. {ECO:0000269 PubMed:26494905}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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 22 64
  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 4 64
  3. Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. (PMID: 26494905) DeLuca A.P. … Slusarski D.C. (Hum. Mol. Genet. 2015) 3 4 64
  4. Mutations in TRNT1 cause congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD). (PMID: 25193871) Chakraborty P.K. … Fleming M.D. (Blood 2014) 3 4 64
  5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64

Products for TRNT1 Gene

Sources for TRNT1 Gene

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