vars1 valyl-tRNA synthetase 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: vars1provided by ZNC
Official Full Name: valyl-tRNA synthetase 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-010601-1
See related: Ensembl:ENSDARG00000044575 AllianceGenome:ZFIN:ZDB-GENE-010601-1
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: vars; vars2; CHUNP6879; im:7137378; wu:fb07a11; wu:fb07d10
Summary: Predicted to enable valine-tRNA ligase activity. Predicted to be involved in valyl-tRNA aminoacylation. Predicted to act upstream of or within tRNA aminoacylation for protein translation. Predicted to be active in cytosol. Is expressed in digestive system; immature eye; intermediate cell mass of mesoderm; nervous system; and somite. Orthologous to human VARS1 (valyl-tRNA synthetase 1). [provided by Alliance of Genome Resources, Oct 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 16

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	16	NC_007127.7 (10429879..10475815)
105	previous assembly	GRCz10 (GCF_000002035.5)	16	NC_007127.6 (10538977..10584913)

Chromosome 16 - NC_007127.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Authors report an allelic series consisting of seven novel and two previously reported biallelic variants in valyl-tRNA synthetase (VARS) in ten patients with a developmental encephalopathy with microcephaly, often associated with early-onset epilepsy.
Title: Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

fi76a04.x1 (e-PCR)
- UniSTS:197994

AI384312 (e-PCR)
- UniSTS:206733

fb07a11.x1 (e-PCR)
- UniSTS:202723

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables aminoacyl-tRNA editing activity	IEA Inferred from Electronic Annotation more info
enables aminoacyl-tRNA ligase activity	IEA Inferred from Electronic Annotation more info
enables ligase activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables valine-tRNA ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables valine-tRNA ligase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within tRNA aminoacylation for protein translation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within translation	IEA Inferred from Electronic Annotation more info
involved_in valyl-tRNA aminoacylation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within valyl-tRNA aminoacylation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: valine--tRNA ligase

Names: valyl-tRNA synthetase 2

NP_001298275.1

EC 6.1.1.9

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.

mRNA and Protein(s)

NM_001311346.1 → NP_001298275.1 valine--tRNA ligase

Status: VALIDATED

Source sequence(s)

CU929328

UniProtKB/TrEMBL

A0A8M1P7Y5, F1Q740

Related

ENSDARP00000142328.1, ENSDART00000173132.2

Conserved Domains (7) summary

cd07962
Location:941 → 1081

Anticodon_Ia_Val; Anticodon-binding domain of valyl tRNA synthetases

cd00817
Location:340 → 941

ValRS_core; catalytic core domain of valyl-tRNA synthetases

cd10294
Location:80 → 202

GST_C_ValRS_N; Glutathione S-transferase C-terminal-like, alpha helical domain of vertebrate Valyl-tRNA synthetase

COG0625
Location:45 → 192

GstA; Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]

PTZ00419
Location:291 → 1270

PTZ00419; valyl-tRNA synthetase-like protein; Provisional

pfam10458
Location:1203 → 1266

Val_tRNA-synt_C; Valyl tRNA synthetase tRNA binding arm

pfam13603
Location:518 → 643

tRNA-synt_1_2; Leucyl-tRNA synthetase, Domain 2