TRIT1 tRNA isopentenyltransferase 1 [Homo sapiens (human)] - Gene

Summary

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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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?

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.
TRIT1 deficiency: Two novel patients with four novel variants.
Title: TRIT1 deficiency: Two novel patients with four novel variants.
The Effect of tRNA([Ser]Sec) Isopentenylation on Selenoprotein Expression.
Title: The Effect of tRNA([Ser]Sec) Isopentenylation on Selenoprotein Expression.
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.
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.
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.
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.
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.
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.
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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S1598 (e-PCR), detects polymorphism
- UniSTS:15638

SHGC-74639 (e-PCR)
- UniSTS:36183

HSC2EC052 (e-PCR)
- UniSTS:60562

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 more info	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

EC 2.5.1.75

NP_001299621.1

EC 2.5.1.75

NP_060116.2

EC 2.5.1.75

XP_047279181.1

EC 2.5.1.75

XP_054193180.1

EC 2.5.1.75

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

NG_042822.2 RefSeqGene

Range

5007..50401

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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

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
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
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
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
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
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
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
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
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
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
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
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
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
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