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_3 g2042 g2042.t4 TSS g2042.t4 14806093 14806093
chr_3 g2042 g2042.t4 isoform g2042.t4 14806107 14807619
chr_3 g2042 g2042.t4 exon g2042.t4.exon1 14806107 14807338
chr_3 g2042 g2042.t4 cds g2042.t4.CDS1 14806676 14807338
chr_3 g2042 g2042.t4 exon g2042.t4.exon2 14807484 14807619
chr_3 g2042 g2042.t4 cds g2042.t4.CDS2 14807484 14807564
chr_3 g2042 g2042.t4 TTS g2042.t4 NA NA

Sequences

>g2042.t4 Gene=g2042 Length=1368
ATGATAGAACAAATTAAAGAATTATCAATTACTGAGGATATTATAACTCCATGGAGTGTT
CAAATTGCTAATAGTGATGGTATTGATTATAACAAATTACTCGAGAAAATTGGTATGAGC
AGAATAAATGCAGATCTTGTAAAAAAATTTGAAAATGTCACTGGAAAAGCAGCTCATTAT
TTCTTTAGAAGAGAAATTTTAATTGCTCATCGAGATTTCGATAAATGTCTTGATTTATAT
GCTGAAAAGAAACCATTCTATTTATACACTGGTATATGTCCTGCAGAGTCTCTTCATTTG
GGTCATTTCATTCAATTTTACATATCAAAGTAAGTTTAACATCAACAATTGCAATTTGTG
ATGCAATATTTTTAATAAATTTCCTTTAAAGGTGGCTTCAAGATGTATTCGATATTCCAG
TCATTATTCAAATTACTGATGATGAAAAAATATTATGGAATGATCTTAAACCTGATGTCT
TGCCAAAATTAGTTAAAGAGACAGTAAAAAATTTGATTGCATTTAACTTCAATCCTGCAA
AAACATTCATCTTTTCAAATTTCAATTATATGGGACAAACACCAGAATATTATAGAAATG
TGATTAGAGTTCGAAAGAGTGTTACTTATGGACAAATTAAAAATACTTTTGGATTCACAG
ATTCAGATCCAATTGGAAAAATAGTTTTCCCATCGCTTCAATTAGTTCCAGCTTTATCGA
CAAGCTTTCCTGAAATTTTTGGCAATGAAAAAGTGCAGCCTATTATTGTATCTGGTCTTG
ATCAAGAACCATATATTCGATTAATGCATGAAATATCGCAAAAACTTGATTTTCCAACAC
CAATTTCGATTCATTCAATATTTTTTCCTGCATTGCATGGAGTTCGAACAAAAATGTCAA
CGAGTGATGTCAATACTGCCATATTTTTGTCAGACACAGCTAAGCAAATTAAGACAAAAA
TTAATAAGCATGCTTTTTCTGGTGGTCGTGTGACAGTAGAGGAACATAGAGAATTTGGTG
GTGATACAAATGTCGATGTTTCTTATCACTTACTGAAATTTTTCCAATCTAATGATGATG
AATTGGAAAAGATAAGATCAACATATAGTTCTGGTGAATTGCTCAGTGGAGAAATTAAAA
AACACGCATTTGAATGCATCCAAGAAATTGTCGCCACTCATCAGGAAACTAAGAAAACTA
TTACGGATGATATTATTGATCAATTCGTAAAGCCTTTAAAAACGGAAGAAATGAGATGTC
ATTCTCTTTCTATATTTGCTTCCTTTTTTCCACAACTTAATAATAATTCTTAATAATATG
TGTGTTTCTTTATGTTACCAACTTTCAATGAAAATATTTTTTATAAAC

>g2042.t4 Gene=g2042 Length=247
MGQTPEYYRNVIRVRKSVTYGQIKNTFGFTDSDPIGKIVFPSLQLVPALSTSFPEIFGNE
KVQPIIVSGLDQEPYIRLMHEISQKLDFPTPISIHSIFFPALHGVRTKMSTSDVNTAIFL
SDTAKQIKTKINKHAFSGGRVTVEEHREFGGDTNVDVSYHLLKFFQSNDDELEKIRSTYS
SGELLSGEIKKHAFECIQEIVATHQETKKTITDDIIDQFVKPLKTEEMRCHSLSIFASFF
PQLNNNS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2042.t4 Gene3D G3DSA:3.40.50.620 HUPs 1 111 0
5 g2042.t4 Gene3D G3DSA:1.10.240.10 - 112 237 0
2 g2042.t4 PANTHER PTHR10055:SF1 TRYPTOPHAN–TRNA LIGASE, CYTOPLASMIC 7 225 0
3 g2042.t4 PANTHER PTHR10055 TRYPTOPHANYL-TRNA SYNTHETASE 7 225 0
1 g2042.t4 Pfam PF00579 tRNA synthetases class I (W and Y) 65 200 0
4 g2042.t4 SUPERFAMILY SSF52374 Nucleotidylyl transferase 3 221 0
7 g2042.t4 TIGRFAM TIGR00233 trpS: tryptophan–tRNA ligase 4 224 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