Gene loci information

Transcript annotation

  • This transcript has been annotated as Tryptophan–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_1 g13952 g13952.t6 TSS g13952.t6 33574101 33574101
chr_1 g13952 g13952.t6 isoform g13952.t6 33574735 33575608
chr_1 g13952 g13952.t6 exon g13952.t6.exon1 33574735 33574909
chr_1 g13952 g13952.t6 cds g13952.t6.CDS1 33574767 33574909
chr_1 g13952 g13952.t6 exon g13952.t6.exon2 33574963 33575608
chr_1 g13952 g13952.t6 cds g13952.t6.CDS2 33574963 33575608
chr_1 g13952 g13952.t6 TTS g13952.t6 33575671 33575671

Sequences

>g13952.t6 Gene=g13952 Length=821
AAGAAGCTTTTAATGTACCACTTGTGATTCAAATGTCTGACGATGAAAAAGTTATATGGA
AAGACTTACCTGTAGAAGAGGGTATTAGATTATCAATTGAAAATGCAAGAGATATTATTG
CTATGGGTTTCGATATTGAAAAGACTTTTATTTTTTCAAATTTATGTTATATGGGACAAT
GTCCAGAATATTACAAAAACATTGTGAAAATTGAAAAGTGTGTGACATATAATCAAGTTA
AAGGAATTTTTGGATTTATTGAGGATGATGTGCTAGGAAAAGTTGGATTTCCTGCTGTTG
AGGCTGCACCAGCTTTATCGACATCTTTTCCATTCATTTTTGGTGACAAAAAACGTCAAG
TGTTAATTCCATGTGCTATTGATCAAGACCCATACTTTCGCATGCTTAGAGATGTTGCTC
CACGCCTTGGTTTTGCAAAGCCTGCCCTCTTACATTCAACTTTTTTTCCTGCATTGCAAG
GAGCTAAATCGAAAATGTCAGCGAGCAATTTTAATTCAGCAATTTTCTTAACTGATACTC
AAGAAGAAATTGCCATGAAAATTAACGATCACACCTTCACAGCAGAAGGAAATGTTGACA
TCGATGTTCCTTACAAACTCCTCACATTCTTTCTTTCTGACGACAATGAATTGGAACGAG
TAAAGAATGCATTCAGTTCTGGTCAAATGTCATCAGCAGAAATTCGAAAAATTGCAATCG
ATTGTTTGCAGCCAATTGTTCGTGAGCACCAAGAAAAAAGGAAACTTGTAACGGATGAAG
TTGTCGAACAATATATGACAGTTAGAAAATTGAATTGCTAG

>g13952.t6 Gene=g13952 Length=262
MSDDEKVIWKDLPVEEGIRLSIENARDIIAMGFDIEKTFIFSNLCYMGQCPEYYKNIVKI
EKCVTYNQVKGIFGFIEDDVLGKVGFPAVEAAPALSTSFPFIFGDKKRQVLIPCAIDQDP
YFRMLRDVAPRLGFAKPALLHSTFFPALQGAKSKMSASNFNSAIFLTDTQEEIAMKINDH
TFTAEGNVDIDVPYKLLTFFLSDDNELERVKNAFSSGQMSSAEIRKIAIDCLQPIVREHQ
EKRKLVTDEVVEQYMTVRKLNC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13952.t6 Gene3D G3DSA:3.40.50.620 HUPs 1 165 0
8 g13952.t6 Gene3D G3DSA:1.10.240.10 - 166 262 0
2 g13952.t6 PANTHER PTHR10055:SF1 TRYPTOPHAN–TRNA LIGASE, CYTOPLASMIC 1 261 0
3 g13952.t6 PANTHER PTHR10055 TRYPTOPHANYL-TRNA SYNTHETASE 1 261 0
6 g13952.t6 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 27 46 0
4 g13952.t6 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 110 131 0
5 g13952.t6 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 154 164 0
1 g13952.t6 Pfam PF00579 tRNA synthetases class I (W and Y) 113 244 0
7 g13952.t6 SUPERFAMILY SSF52374 Nucleotidylyl transferase 2 258 0
10 g13952.t6 TIGRFAM TIGR00233 trpS: tryptophan–tRNA ligase 2 256 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:0004830 tryptophan-tRNA ligase activity MF
GO:0005524 ATP binding MF
GO:0006436 tryptophanyl-tRNA aminoacylation BP
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