General information for g2042.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tryptophan–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g2042 is located on chr_3: 14806930..14816114 (+ strand)
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.t5 | TSS | g2042.t5 | 14806093 | 14806093 |
| chr_3 | g2042 | g2042.t5 | isoform | g2042.t5 | 14806501 | 14807420 |
| chr_3 | g2042 | g2042.t5 | exon | g2042.t5.exon1 | 14806501 | 14807420 |
| chr_3 | g2042 | g2042.t5 | cds | g2042.t5.CDS1 | 14806676 | 14807356 |
| chr_3 | g2042 | g2042.t5 | TTS | g2042.t5 | 14807433 | 14807433 |
Sequences
>g2042.t5 Gene=g2042 Length=920
GCTTCAAGATGTATTCGATATTCCAGTCATTATTCAAATTACTGATGATGAAAAAATATT
ATGGAATGATCTTAAACCTGATGTCTTGCCAAAATTAGTTAAAGAGACAGTAAAAAATTT
GATTGCATTTAACTTCAATCCTGCAAAAACATTCATCTTTTCAAATTTCAATTATATGGG
ACAAACACCAGAATATTATAGAAATGTGATTAGAGTTCGAAAGAGTGTTACTTATGGACA
AATTAAAAATACTTTTGGATTCACAGATTCAGATCCAATTGGAAAAATAGTTTTCCCATC
GCTTCAATTAGTTCCAGCTTTATCGACAAGCTTTCCTGAAATTTTTGGCAATGAAAAAGT
GCAGCCTATTATTGTATCTGGTCTTGATCAAGAACCATATATTCGATTAATGCATGAAAT
ATCGCAAAAACTTGATTTTCCAACACCAATTTCGATTCATTCAATATTTTTTCCTGCATT
GCATGGAGTTCGAACAAAAATGTCAACGAGTGATGTCAATACTGCCATATTTTTGTCAGA
CACAGCTAAGCAAATTAAGACAAAAATTAATAAGCATGCTTTTTCTGGTGGTCGTGTGAC
AGTAGAGGAACATAGAGAATTTGGTGGTGATACAAATGTCGATGTTTCTTATCACTTACT
GAAATTTTTCCAATCTAATGATGATGAATTGGAAAAGATAAGATCAACATATAGTTCTGG
TGAATTGCTCAGTGGAGAAATTAAAAAACACGCATTTGAATGCATCCAAGAAATTGTCGC
CACTCATCAGGAAACTAAGAAAACTATTACGGATGATATTATTGATCAATTCGTAAAGCC
TAAAAATATGAAATAATTTATTTGTGTATGCTTAAAAAAGATTATGAAAGGAAAATAATA
AAAAAACATGCATACTGTTT
>g2042.t5 Gene=g2042 Length=226
MGQTPEYYRNVIRVRKSVTYGQIKNTFGFTDSDPIGKIVFPSLQLVPALSTSFPEIFGNE
KVQPIIVSGLDQEPYIRLMHEISQKLDFPTPISIHSIFFPALHGVRTKMSTSDVNTAIFL
SDTAKQIKTKINKHAFSGGRVTVEEHREFGGDTNVDVSYHLLKFFQSNDDELEKIRSTYS
SGELLSGEIKKHAFECIQEIVATHQETKKTITDDIIDQFVKPKNMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2042.t5 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 111 | 0 |
| 5 | g2042.t5 | Gene3D | G3DSA:1.10.240.10 | - | 112 | 226 | 0 |
| 2 | g2042.t5 | PANTHER | PTHR10055:SF1 | TRYPTOPHAN–TRNA LIGASE, CYTOPLASMIC | 7 | 225 | 0 |
| 3 | g2042.t5 | PANTHER | PTHR10055 | TRYPTOPHANYL-TRNA SYNTHETASE | 7 | 225 | 0 |
| 1 | g2042.t5 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 65 | 200 | 0 |
| 4 | g2042.t5 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 3 | 223 | 0 |
| 7 | g2042.t5 | 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.
