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.t3 TSS g2042.t3 14806093 14806093
chr_3 g2042 g2042.t3 isoform g2042.t3 14806107 14807356
chr_3 g2042 g2042.t3 exon g2042.t3.exon1 14806107 14806435
chr_3 g2042 g2042.t3 cds g2042.t3.CDS1 14806107 14806435
chr_3 g2042 g2042.t3 exon g2042.t3.exon2 14806498 14806858
chr_3 g2042 g2042.t3 cds g2042.t3.CDS2 14806498 14806858
chr_3 g2042 g2042.t3 exon g2042.t3.exon3 14806974 14807356
chr_3 g2042 g2042.t3 cds g2042.t3.CDS3 14806974 14807099
chr_3 g2042 g2042.t3 TTS g2042.t3 14807433 14807433

Sequences

>g2042.t3 Gene=g2042 Length=1073
ATGATAGAACAAATTAAAGAATTATCAATTACTGAGGATATTATAACTCCATGGAGTGTT
CAAATTGCTAATAGTGATGGTATTGATTATAACAAATTACTCGAGAAAATTGGTATGAGC
AGAATAAATGCAGATCTTGTAAAAAAATTTGAAAATGTCACTGGAAAAGCAGCTCATTAT
TTCTTTAGAAGAGAAATTTTAATTGCTCATCGAGATTTCGATAAATGTCTTGATTTATAT
GCTGAAAAGAAACCATTCTATTTATACACTGGTATATGTCCTGCAGAGTCTCTTCATTTG
GGTCATTTCATTCAATTTTACATATCAAAGTGGCTTCAAGATGTATTCGATATTCCAGTC
ATTATTCAAATTACTGATGATGAAAAAATATTATGGAATGATCTTAAACCTGATGTCTTG
CCAAAATTAGTTAAAGAGACAGTAAAAAATTTGATTGCATTTAACTTCAATCCTGCAAAA
ACATTCATCTTTTCAAATTTCAATTATATGGGACAAACACCAGAATATTATAGAAATGTG
ATTAGAGTTCGAAAGAGTGTTACTTATGGACAAATTAAAAATACTTTTGGATTCACAGAT
TCAGATCCAATTGGAAAAATAGTTTTCCCATCGCTTCAATTAGTTCCAGCTTTATCGACA
AGCTTTCCTGAAATTTTTGGCAATGAAAAACTGCATTGCATGGAGTTCGAACAAAAATGT
CAACGAGTGATGTCAATACTGCCATATTTTTGTCAGACACAGCTAAGCAAATTAAGACAA
AAATTAATAAGCATGCTTTTTCTGGTGGTCGTGTGACAGTAGAGGAACATAGAGAATTTG
GTGGTGATACAAATGTCGATGTTTCTTATCACTTACTGAAATTTTTCCAATCTAATGATG
ATGAATTGGAAAAGATAAGATCAACATATAGTTCTGGTGAATTGCTCAGTGGAGAAATTA
AAAAACACGCATTTGAATGCATCCAAGAAATTGTCGCCACTCATCAGGAAACTAAGAAAA
CTATTACGGATGATATTATTGATCAATTCGTAAAGCCTAAAAATATGAAATAA

>g2042.t3 Gene=g2042 Length=271
MIEQIKELSITEDIITPWSVQIANSDGIDYNKLLEKIGMSRINADLVKKFENVTGKAAHY
FFRREILIAHRDFDKCLDLYAEKKPFYLYTGICPAESLHLGHFIQFYISKWLQDVFDIPV
IIQITDDEKILWNDLKPDVLPKLVKETVKNLIAFNFNPAKTFIFSNFNYMGQTPEYYRNV
IRVRKSVTYGQIKNTFGFTDSDPIGKIVFPSLQLVPALSTSFPEIFGNEKLHCMEFEQKC
QRVMSILPYFCQTQLSKLRQKLISMLFLVVV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g2042.t3 Gene3D G3DSA:3.40.50.620 HUPs 7 241 3.4E-83
1 g2042.t3 PANTHER PTHR10055:SF1 TRYPTOPHAN–TRNA LIGASE, CYTOPLASMIC 12 234 5.2E-79
2 g2042.t3 PANTHER PTHR10055 TRYPTOPHANYL-TRNA SYNTHETASE 12 234 5.2E-79
4 g2042.t3 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 94 103 -
3 g2042.t3 SUPERFAMILY SSF52374 Nucleotidylyl transferase 13 228 8.75E-47

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. There were no conditions that were differentially expressed