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TRIT1 tRNA isopentenyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 54802, updated on 2-Nov-2024

Summary

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Official Symbol
TRIT1provided by HGNC
Official Full Name
tRNA isopentenyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:20286
See related
Ensembl:ENSG00000043514 MIM:617840; AllianceGenome:HGNC:20286
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IPT; GRO1; IPPT; MOD5; hGRO1; IPTase; COXPD35
Summary
This gene encodes a protein that that is targeted to the mitochondrion and modifies transfer RNAs (tRNAs) by adding a dimethylallyl group onto the adenine at position 37. This modification is important for maintaining the correct reading frame during protein translation. This gene is considered a tumor suppressor and its expression can decrease cell growth. Alternative splicing results in multiple transcripts variants, most of which are likely non-functional. [provided by RefSeq, Aug 2015]
Expression
Ubiquitous expression in thyroid (RPKM 7.3), prostate (RPKM 6.7) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See TRIT1 in Genome Data Viewer
Location:
1p34.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (39838110..39883511, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39707546..39752951, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40303782..40349183, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC130932201 Neighboring gene long intergenic non-protein coding RNA 2811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40282415-40283410 Neighboring gene uncharacterized LOC105378667 Neighboring gene MPRA-validated peak189 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40348408-40349228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40349229-40350047 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:40353876-40354074 Neighboring gene MYCL antisense RNA 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:40363871-40364442 Neighboring gene Sharpr-MPRA regulatory region 6057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 716 Neighboring gene MYCL proto-oncogene, bHLH transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40409912-40410434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 823 Neighboring gene MFSD2 lysolipid transporter A, lysophospholipid Neighboring gene ribosomal protein S2 pseudogene 12

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRIT1 defect leads to a recognizable phenotype of myoclonic epilepsy, speech delay, strabismus, progressive spasticity, and normal lactate levels.
    Title: TRIT1 defect leads to a recognizable phenotype of myoclonic epilepsy, speech delay, strabismus, progressive spasticity, and normal lactate levels.
  2. TRIT1 deficiency: Two novel patients with four novel variants.
    Title: TRIT1 deficiency: Two novel patients with four novel variants.
  3. The Effect of tRNA([Ser]Sec) Isopentenylation on Selenoprotein Expression.
    Title: The Effect of tRNA([Ser]Sec) Isopentenylation on Selenoprotein Expression.
  4. Targeting mitochondrial and cytosolic substrates of TRIT1 isopentenyltransferase: Specificity determinants and tRNA-i6A37 profiles
    Title: Targeting mitochondrial and cytosolic substrates of TRIT1 isopentenyltransferase: Specificity determinants and tRNA-i6A37 profiles.
  5. We show that dysfunctional TRIT1 results in decreased levels of select mitochondrial proteins. Our findings confirm the TRIT1 disease association and advance the phenotypic and molecular understanding of this disorder.
    Title: Matchmaking facilitates the diagnosis of an autosomal-recessive mitochondrial disease caused by biallelic mutation of the tRNA isopentenyltransferase (TRIT1) gene.
  6. characterize TRIT1 as a novel human amyloid fiber forming protein. We discuss these data in light of TRIT1's functional roles and possible implications for disease
    Title: The human tRNA-modifying protein, TRIT1, forms amyloid fibers in vitro.
  7. patient cells bearing the p.Arg323Gln TRIT1 mutation are severely deficient in i6A37 in both cytosolic and mitochondrial tRNAs
    Title: Defective i6A37 modification of mitochondrial and cytosolic tRNAs results from pathogenic mutations in TRIT1 and its substrate tRNA.
  8. In light of this additional nuclear role for Mod5 we discuss the proposed role of the human homologue of Mod5, TRIT1, as a tumor suppressor protein.[review]
    Title: The cytoplasmic and nuclear populations of the eukaryote tRNA-isopentenyl transferase have distinct functions with implications in human cancer.
  9. TRIT1 may control the levels of some tRNAs as well as their specific activity.
    Title: Human cells have a limited set of tRNA anticodon loop substrates of the tRNA isopentenyltransferase TRIT1 tumor suppressor.
  10. One TRIT1 haplotype, CCGT, was associated with lymph node metastasis.
    Title: Association of polymorphisms and haplotype in the region of TRIT1, MYCL1 and MFSD2A with the risk and clinicopathological features of gastric cancer in a southeast Chinese population.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Combined oxidative phosphorylation deficiency 35
MedGen: C4693466 OMIM: 617873 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20061, MGC149242, MGC149243

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tRNA dimethylallyltransferase activity EXP
Inferred from Experiment
more info
 PubMed 
enables tRNA dimethylallyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables tRNA dimethylallyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA dimethylallyltransferase activity TAS
Traceable Author Statement
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in mitochondrial tRNA modification IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitochondrial tRNA modification TAS
Traceable Author Statement
more info
  
involved_in tRNA modification IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA modification IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
tRNA dimethylallyltransferase
Names
IPP transferase
isopentenyl-diphosphate:tRNA isopentenyltransferase
tRNA dimethylallyltransferase, mitochondrial
tRNA isopentenylpyrophosphate transferase
NP_001299620.1
NP_001299621.1
NP_060116.2
XP_047279181.1
XP_054193180.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_042822.2 RefSeqGene

    Range
    5007..50401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001312691.1 → NP_001299620.1  tRNA dimethylallyltransferase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (16) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK223478, AY052768, BC010741, BE294565
    Consensus CDS
    CCDS81303.1
    UniProtKB/TrEMBL
    Q53F11
    Related
    ENSP00000361905.1, ENST00000372818.5
    Conserved Domains (3) summary
    smart00451
    Location:369 → 400
    ZnF_U1; U1-like zinc finger
    PRK00091
    Location:24 → 310
    miaA; tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
    pfam13304
    Location:25 → 203
    AAA_21; AAA domain, putative AbiEii toxin, Type IV TA system

  2. NM_001312692.1 → NP_001299621.1  tRNA dimethylallyltransferase isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (17) lacks two alternate in-frame exons and uses an alternate in-frame splice site compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AK223478, BC010741, BE294565
    Consensus CDS
    CCDS81302.1
    UniProtKB/TrEMBL
    Q53F11
    Related
    ENSP00000388333.2, ENST00000441669.6
    Conserved Domains (2) summary
    smart00451
    Location:313 → 344
    ZnF_U1; U1-like zinc finger
    cl21455
    Location:24 → 251
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  3. NM_017646.6 → NP_060116.2  tRNA dimethylallyltransferase isoform 1 precursor

    See identical proteins and their annotated locations for NP_060116.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest functional protein (isoform 1).
    Source sequence(s)
    AK223478, AL033527, AY702933, BE294565
    Consensus CDS
    CCDS30681.1
    UniProtKB/Swiss-Prot
    A1A4X7, Q3T7B5, Q5QPK5, Q5QPK6, Q6IAC9, Q96FJ3, Q96L45, Q9H3H1, Q9NXT7
    UniProtKB/TrEMBL
    Q53F11
    Related
    ENSP00000321810.5, ENST00000316891.10
    Conserved Domains (3) summary
    smart00451
    Location:395 → 426
    ZnF_U1; U1-like zinc finger
    PRK00091
    Location:24 → 333
    miaA; tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
    pfam13304
    Location:25 → 203
    AAA_21; AAA domain, putative AbiEii toxin, Type IV TA system

RNA

  1. NR_132401.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702934, BE294565
    Related
    ENST00000462797.5

  2. NR_132402.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702936, BE294565

  3. NR_132403.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate internal exon and uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702937, BE294565

  4. NR_132404.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an alternate internal exon and uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702938, BE294565

  5. NR_132405.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate internal exon and uses alternate splice site in two internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702939, BE294565

  6. NR_132406.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks two alternate internal exons and uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702940, BE294565

  7. NR_132407.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks three alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702941, BE294565

  8. NR_132408.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) lacks three alternate internal exons and uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702942, BE294565

  9. NR_132409.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) lacks four alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702943, BE294565

  10. NR_132410.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12) lacks four alternate internal exons and uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702944, BE294565

  11. NR_132412.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (13) lacks five alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702945, BE294565

  12. NR_132413.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (14) lacks seven alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK223478, AY702946, BE294565

  13. NR_132414.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (15) lacks nine alternate internal exons compared to variant 1. This variant is represented as non-coding because it lacks almost all the reading frame found in variant 1.
    Source sequence(s)
    AK223478, AY702947, BE294565

  14. NR_132415.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (18) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF074918, AK223478, BE294565
    Related
    ENST00000537440.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    39838110..39883511 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423225.1 → XP_047279181.1  tRNA dimethylallyltransferase isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    39707546..39752951 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337205.1 → XP_054193180.1  tRNA dimethylallyltransferase isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H3H1.1 GenPept UniProtKB/Swiss-Prot:Q9H3H1

Gene LinkOut

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