General information for g2042.t1
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.t1 | TSS | g2042.t1 | 14806093 | 14806093 |
| chr_3 | g2042 | g2042.t1 | isoform | g2042.t1 | 14806107 | 14807356 |
| chr_3 | g2042 | g2042.t1 | exon | g2042.t1.exon1 | 14806107 | 14806435 |
| chr_3 | g2042 | g2042.t1 | cds | g2042.t1.CDS1 | 14806107 | 14806435 |
| chr_3 | g2042 | g2042.t1 | exon | g2042.t1.exon2 | 14806498 | 14807356 |
| chr_3 | g2042 | g2042.t1 | cds | g2042.t1.CDS2 | 14806498 | 14807356 |
| chr_3 | g2042 | g2042.t1 | TTS | g2042.t1 | 14807433 | 14807433 |
Sequences
>g2042.t1 Gene=g2042 Length=1188
ATGATAGAACAAATTAAAGAATTATCAATTACTGAGGATATTATAACTCCATGGAGTGTT
CAAATTGCTAATAGTGATGGTATTGATTATAACAAATTACTCGAGAAAATTGGTATGAGC
AGAATAAATGCAGATCTTGTAAAAAAATTTGAAAATGTCACTGGAAAAGCAGCTCATTAT
TTCTTTAGAAGAGAAATTTTAATTGCTCATCGAGATTTCGATAAATGTCTTGATTTATAT
GCTGAAAAGAAACCATTCTATTTATACACTGGTATATGTCCTGCAGAGTCTCTTCATTTG
GGTCATTTCATTCAATTTTACATATCAAAGTGGCTTCAAGATGTATTCGATATTCCAGTC
ATTATTCAAATTACTGATGATGAAAAAATATTATGGAATGATCTTAAACCTGATGTCTTG
CCAAAATTAGTTAAAGAGACAGTAAAAAATTTGATTGCATTTAACTTCAATCCTGCAAAA
ACATTCATCTTTTCAAATTTCAATTATATGGGACAAACACCAGAATATTATAGAAATGTG
ATTAGAGTTCGAAAGAGTGTTACTTATGGACAAATTAAAAATACTTTTGGATTCACAGAT
TCAGATCCAATTGGAAAAATAGTTTTCCCATCGCTTCAATTAGTTCCAGCTTTATCGACA
AGCTTTCCTGAAATTTTTGGCAATGAAAAAGTGCAGCCTATTATTGTATCTGGTCTTGAT
CAAGAACCATATATTCGATTAATGCATGAAATATCGCAAAAACTTGATTTTCCAACACCA
ATTTCGATTCATTCAATATTTTTTCCTGCATTGCATGGAGTTCGAACAAAAATGTCAACG
AGTGATGTCAATACTGCCATATTTTTGTCAGACACAGCTAAGCAAATTAAGACAAAAATT
AATAAGCATGCTTTTTCTGGTGGTCGTGTGACAGTAGAGGAACATAGAGAATTTGGTGGT
GATACAAATGTCGATGTTTCTTATCACTTACTGAAATTTTTCCAATCTAATGATGATGAA
TTGGAAAAGATAAGATCAACATATAGTTCTGGTGAATTGCTCAGTGGAGAAATTAAAAAA
CACGCATTTGAATGCATCCAAGAAATTGTCGCCACTCATCAGGAAACTAAGAAAACTATT
ACGGATGATATTATTGATCAATTCGTAAAGCCTAAAAATATGAAATAA
>g2042.t1 Gene=g2042 Length=395
MIEQIKELSITEDIITPWSVQIANSDGIDYNKLLEKIGMSRINADLVKKFENVTGKAAHY
FFRREILIAHRDFDKCLDLYAEKKPFYLYTGICPAESLHLGHFIQFYISKWLQDVFDIPV
IIQITDDEKILWNDLKPDVLPKLVKETVKNLIAFNFNPAKTFIFSNFNYMGQTPEYYRNV
IRVRKSVTYGQIKNTFGFTDSDPIGKIVFPSLQLVPALSTSFPEIFGNEKVQPIIVSGLD
QEPYIRLMHEISQKLDFPTPISIHSIFFPALHGVRTKMSTSDVNTAIFLSDTAKQIKTKI
NKHAFSGGRVTVEEHREFGGDTNVDVSYHLLKFFQSNDDELEKIRSTYSSGELLSGEIKK
HAFECIQEIVATHQETKKTITDDIIDQFVKPKNMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2042.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 7 | 280 | 2.0E-98 |
| 10 | g2042.t1 | Gene3D | G3DSA:1.10.240.10 | - | 281 | 395 | 9.4E-47 |
| 2 | g2042.t1 | PANTHER | PTHR10055:SF1 | TRYPTOPHAN–TRNA LIGASE, CYTOPLASMIC | 12 | 394 | 4.3E-148 |
| 3 | g2042.t1 | PANTHER | PTHR10055 | TRYPTOPHANYL-TRNA SYNTHETASE | 12 | 394 | 4.3E-148 |
| 7 | g2042.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 98 | 114 | 6.9E-12 |
| 6 | g2042.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 150 | 169 | 6.9E-12 |
| 4 | g2042.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 233 | 254 | 6.9E-12 |
| 5 | g2042.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 277 | 287 | 6.9E-12 |
| 1 | g2042.t1 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 83 | 369 | 5.0E-16 |
| 9 | g2042.t1 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 94 | 103 | - |
| 8 | g2042.t1 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 13 | 392 | 1.25E-87 |
| 12 | g2042.t1 | TIGRFAM | TIGR00233 | trpS: tryptophan–tRNA ligase | 84 | 393 | 2.2E-77 |
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 transcript has been annotated with K01867 (tryptophanyl-tRNA synthetase)
Pathway
- This transcript belongs to the following pathways
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.
