Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Valine–tRNA ligase, mitochondrial 1.

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_2 g7483 g7483.t5 TSS g7483.t5 23967942 23967942
chr_2 g7483 g7483.t5 isoform g7483.t5 23967966 23968462
chr_2 g7483 g7483.t5 exon g7483.t5.exon1 23967966 23968462
chr_2 g7483 g7483.t5 cds g7483.t5.CDS1 23968093 23968461
chr_2 g7483 g7483.t5 TTS g7483.t5 23968458 23968458

Sequences

>g7483.t5 Gene=g7483 Length=497
ATGATCTTTAAATATCAAAATTTTAACATTACTAAAAATAAAGTAAAAACTATTACACGA
CGGTGTTCAAATTCTTCTTTGCAAAAAGATGTATTTATAAACAGTGAGTATTTAATAATA
CAACTTCATGACATTTTATTATGTACTTTTAGAGCAACTTAAAATTGCCGCATATCAACC
TAAATTAATTGAAAACAAAAATGTCTGGAATATTAGAAATATTCGATCAACATCTAAAGA
GAAGTTTTCAATGATTTTTCCACCGCCAAATGTGACAGGAAATATTCATTTAGGACATGC
ATTAACAGCAACAATTCAAGATGTAATAATTCGATGGAAGAGAAAGCAAAATTTCGACAC
ACAGTGGATATTTGGAACTGATCATGCTGGAATAGCTACTCAATTAATTTTGGAAAAGAT
TTTATTCAAACGAGAGAACAAAACGAGACATGAAATTGGTAGAGAGCAATTTTTAAAAGA
AACATGGAATTGGAAAA

>g7483.t5 Gene=g7483 Length=123
MTFYYVLLEQLKIAAYQPKLIENKNVWNIRNIRSTSKEKFSMIFPPPNVTGNIHLGHALT
ATIQDVIIRWKRKQNFDTQWIFGTDHAGIATQLILEKILFKRENKTRHEIGREQFLKETW
NWK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7483.t5 Gene3D G3DSA:3.40.50.620 HUPs 28 123 1.5E-28
2 g7483.t5 PANTHER PTHR11946:SF62 RE41093P 14 123 3.5E-41
3 g7483.t5 PANTHER PTHR11946 VALYL-TRNA SYNTHETASES 14 123 3.5E-41
1 g7483.t5 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 23 123 2.1E-31
5 g7483.t5 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 47 58 -
4 g7483.t5 SUPERFAMILY SSF52374 Nucleotidylyl transferase 15 122 9.19E-29

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