Gene loci information

Transcript annotation

  • This transcript has been annotated as Valine–tRNA ligase.

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 g3578 g3578.t17 TSS g3578.t17 26525057 26525057
chr_3 g3578 g3578.t17 isoform g3578.t17 26525096 26526053
chr_3 g3578 g3578.t17 exon g3578.t17.exon1 26525096 26525260
chr_3 g3578 g3578.t17 cds g3578.t17.CDS1 26525096 26525260
chr_3 g3578 g3578.t17 exon g3578.t17.exon2 26525336 26525503
chr_3 g3578 g3578.t17 cds g3578.t17.CDS2 26525336 26525503
chr_3 g3578 g3578.t17 exon g3578.t17.exon3 26525560 26525751
chr_3 g3578 g3578.t17 cds g3578.t17.CDS3 26525560 26525751
chr_3 g3578 g3578.t17 exon g3578.t17.exon4 26525810 26526053
chr_3 g3578 g3578.t17 cds g3578.t17.CDS4 26525810 26526052
chr_3 g3578 g3578.t17 TTS g3578.t17 NA NA

Sequences

>g3578.t17 Gene=g3578 Length=769
ATGACTAATGTAAAAACTGATGAAGCTGCAAACGAGGAAGTTGTTGAAAAAAGTGCAAAA
CAACTCGAGAAAGAAGCTAAAAAAGCTGCTAAATTAGCTAAGCTTCAAGAAAAACAAGCA
AAACAGGCTACTCAACAAGCAAATACAGCACCTAAGGAAAAAGAGAAAAAAGCTAAATCT
GTAGTGAAAGACATTATTTATGAAGGAAATTCAAAGGATGGTGAAAAGAAGGATTTATCT
GGACCTATGCCAGAAGCTTACTCGCCTCAATACGTTGAAGCAGCGTGGTATTCTTGGTGG
GAGAAACAAGGATTTTTCAAGCCGGAATATTCTATGAAAAATGGAAAAATATCTTCGAAA
GGTCAATTTGTAATGGTTATTCCACCACCGAATGTTACTGGCTCTTTGCATTTAGGTCAT
GCTTTGACAAATTCTATTGAAGATGCAATTGCAAGATGGCATAGAATGCATGGACGAACA
ACTCTTTGGGTTCCAGGTTGTGACCATGCTGGCATTGCAACTCAAGTAGTCGTAGAGAAA
AAATTGTGGAGAGAAGAGAAACTCAGTCGTCATGATCTTGGTCGAGAAAAGTTTATTGAA
AAAATTTGGGAATGGAAAGAGAACAAGGGAGGTAGAATTTATCATCAATTGAGAAAAATT
GGTTCATCTATGGATTGGGATCGTGTTTCCTTCACAATGGATCCAAAACTTTGTCGTGCT
GTTACTGAAGCTTTCAATCAAATGCATGAAAAGGGTTTGATTTATCGTG

>g3578.t17 Gene=g3578 Length=256
MTNVKTDEAANEEVVEKSAKQLEKEAKKAAKLAKLQEKQAKQATQQANTAPKEKEKKAKS
VVKDIIYEGNSKDGEKKDLSGPMPEAYSPQYVEAAWYSWWEKQGFFKPEYSMKNGKISSK
GQFVMVIPPPNVTGSLHLGHALTNSIEDAIARWHRMHGRTTLWVPGCDHAGIATQVVVEK
KLWREEKLSRHDLGREKFIEKIWEWKENKGGRIYHQLRKIGSSMDWDRVSFTMDPKLCRA
VTEAFNQMHEKGLIYR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3578.t17 Coils Coil Coil 12 46 -
8 g3578.t17 Gene3D G3DSA:3.40.50.620 HUPs 85 256 1.0E-53
7 g3578.t17 MobiDBLite mobidb-lite consensus disorder prediction 1 61 -
6 g3578.t17 MobiDBLite mobidb-lite consensus disorder prediction 9 35 -
2 g3578.t17 PANTHER PTHR11946:SF110 VALINE–TRNA LIGASE 11 256 9.1E-114
3 g3578.t17 PANTHER PTHR11946 VALYL-TRNA SYNTHETASES 11 256 9.1E-114
1 g3578.t17 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 96 256 7.2E-59
5 g3578.t17 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 130 141 -
4 g3578.t17 SUPERFAMILY SSF52374 Nucleotidylyl transferase 82 256 3.94E-52

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:0004812 aminoacyl-tRNA ligase activity MF

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.

Raw TPM values