Gene loci information

Transcript annotation

  • This transcript has been annotated as Tyrosine–tRNA ligase, cytoplasmic.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g1213 g1213.t2 TSS g1213.t2 8797313 8797313
chr_3 g1213 g1213.t2 isoform g1213.t2 8797434 8798182
chr_3 g1213 g1213.t2 exon g1213.t2.exon1 8797434 8797641
chr_3 g1213 g1213.t2 exon g1213.t2.exon2 8797711 8798182
chr_3 g1213 g1213.t2 cds g1213.t2.CDS1 8797753 8798181
chr_3 g1213 g1213.t2 TTS g1213.t2 NA NA

Sequences

>g1213.t2 Gene=g1213 Length=680
ATGGCAGAAGAATTGACATTTGAAAAGAAACTTGAGTTAATCAAAAGAAATCTGCAAGAG
GTTCTTGGTGAAGAAAATCTGCACAAGATTGTGAAAGAACGAGATTTAAAACTTTATTGG
GGAACTGCCACAACTGGAAAACCTCATATTGCATATTTCGTGCCAATGACAAAAATTGCA
GACTTTCTAAAAGCTGGATGTGAAGTGAGTCACAATCTTGTTTGCAGACTTACATGCATA
TTTAGATAATATGAAAGCACCATGGTCACTTCTAGAAGAGAGAACAAAATATTATGAAGC
TGTTATTAAAGCTATGCTTCAATCACTAGGTGTACCATTGGAGAAACTTAAATTCGTGCA
AGGCACAAGTTTTGAATTGTCTCGTGAATACTCTTTAGATGTTTATAGACTCACATCAAT
TGTGACTCAACATGATGCTAAAAAAGCTGGTGCTGAAGTTGTGAAACAAGTTGAATATCC
TCTTTTATCTGGATTGCTTTATCCTGGCCTTCAGGCACTCGATGAAGAATATTTAAAAGT
TGATGCTCAATTTGGAGGTGTTGATCAAAGAAAAATTTTTACTTTTGCTGAAAAATATCT
TCCACAACTCGGTTATGCAAAGAGAATTCATCTTATGAATCCCATGGTGCCTGGTTTAAC
AGGTGGCAAAATGTCTTCTT

>g1213.t2 Gene=g1213 Length=143
MKAPWSLLEERTKYYEAVIKAMLQSLGVPLEKLKFVQGTSFELSREYSLDVYRLTSIVTQ
HDAKKAGAEVVKQVEYPLLSGLLYPGLQALDEEYLKVDAQFGGVDQRKIFTFAEKYLPQL
GYAKRIHLMNPMVPGLTGGKMSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g1213.t2 Gene3D G3DSA:3.40.50.620 HUPs 1 133 0
2 g1213.t2 PANTHER PTHR42765 SOLEUCYL-TRNA SYNTHETASE 1 143 0
3 g1213.t2 PANTHER PTHR42765:SF2 TYROSINE–TRNA LIGASE 1 143 0
5 g1213.t2 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 76 91 0
4 g1213.t2 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 93 115 0
6 g1213.t2 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 126 138 0
1 g1213.t2 Pfam PF00579 tRNA synthetases class I (W and Y) 2 143 0
7 g1213.t2 SUPERFAMILY SSF52374 Nucleotidylyl transferase 6 143 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005524 ATP binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004831 tyrosine-tRNA ligase activity MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0006437 tyrosyl-tRNA aminoacylation BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed