General information for g2042.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t6 | TSS | g2042.t6 | 14806093 | 14806093 |
| chr_3 | g2042 | g2042.t6 | isoform | g2042.t6 | 14806930 | 14816114 |
| chr_3 | g2042 | g2042.t6 | exon | g2042.t6.exon1 | 14806930 | 14807338 |
| chr_3 | g2042 | g2042.t6 | cds | g2042.t6.CDS1 | 14807000 | 14807338 |
| chr_3 | g2042 | g2042.t6 | exon | g2042.t6.exon2 | 14810546 | 14810607 |
| chr_3 | g2042 | g2042.t6 | cds | g2042.t6.CDS2 | 14810546 | 14810587 |
| chr_3 | g2042 | g2042.t6 | exon | g2042.t6.exon3 | 14815977 | 14816114 |
| chr_3 | g2042 | g2042.t6 | TTS | g2042.t6 | NA | NA |
Sequences
>g2042.t6 Gene=g2042 Length=609
ACTTGATTTTCCAACACCAATTTCGATTCATTCAATATTTTTTCCTGCATTGCATGGAGT
TCGAACAAAAATGTCAACGAGTGATGTCAATACTGCCATATTTTTGTCAGACACAGCTAA
GCAAATTAAGACAAAAATTAATAAGCATGCTTTTTCTGGTGGTCGTGTGACAGTAGAGGA
ACATAGAGAATTTGGTGGTGATACAAATGTCGATGTTTCTTATCACTTACTGAAATTTTT
CCAATCTAATGATGATGAATTGGAAAAGATAAGATCAACATATAGTTCTGGTGAATTGCT
CAGTGGAGAAATTAAAAAACACGCATTTGAATGCATCCAAGAAATTGTCGCCACTCATCA
GGAAACTAAGAAAACTATTACGGATGATATTATTGATCAATTCGTAAAGCAATGTTTAGT
GACATCTTTGATTTTTGTGATTGCTTTATAACTTATTAATGGTTGACCATTGTTCTTCAA
AAATTAATTCCTCATCGTAATTAAAATCTTTAATAGTTGGATATTTGCCTACTGCTTCTG
TGCTTTTCCATGTTCCCAACAACGAACGTAAAAACTGATGCATTGCGATCATATATTAAT
TTTTCACTC
>g2042.t6 Gene=g2042 Length=126
MSTSDVNTAIFLSDTAKQIKTKINKHAFSGGRVTVEEHREFGGDTNVDVSYHLLKFFQSN
DDELEKIRSTYSSGELLSGEIKKHAFECIQEIVATHQETKKTITDDIIDQFVKQCLVTSL
IFVIAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2042.t6 | Gene3D | G3DSA:1.10.240.10 | - | 2 | 121 | 0e+00 |
| 2 | g2042.t6 | PANTHER | PTHR10055:SF1 | TRYPTOPHAN–TRNA LIGASE, CYTOPLASMIC | 1 | 114 | 0e+00 |
| 3 | g2042.t6 | PANTHER | PTHR10055 | TRYPTOPHANYL-TRNA SYNTHETASE | 1 | 114 | 0e+00 |
| 1 | g2042.t6 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 1 | 92 | 1e-06 |
| 4 | g2042.t6 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 1 | 113 | 0e+00 |
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.
