General information for g13952.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 g13952 is located on chr_1: 33574961..33575671 (+ 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_1 | g13952 | g13952.t1 | TSS | g13952.t1 | 33574101 | 33574101 |
| chr_1 | g13952 | g13952.t1 | isoform | g13952.t1 | 33574165 | 33575608 |
| chr_1 | g13952 | g13952.t1 | exon | g13952.t1.exon1 | 33574165 | 33574249 |
| chr_1 | g13952 | g13952.t1 | cds | g13952.t1.CDS1 | 33574165 | 33574249 |
| chr_1 | g13952 | g13952.t1 | exon | g13952.t1.exon2 | 33574402 | 33574669 |
| chr_1 | g13952 | g13952.t1 | cds | g13952.t1.CDS2 | 33574402 | 33574669 |
| chr_1 | g13952 | g13952.t1 | exon | g13952.t1.exon3 | 33574727 | 33574909 |
| chr_1 | g13952 | g13952.t1 | cds | g13952.t1.CDS3 | 33574727 | 33574909 |
| chr_1 | g13952 | g13952.t1 | exon | g13952.t1.exon4 | 33574963 | 33575608 |
| chr_1 | g13952 | g13952.t1 | cds | g13952.t1.CDS4 | 33574963 | 33575608 |
| chr_1 | g13952 | g13952.t1 | TTS | g13952.t1 | 33575671 | 33575671 |
Sequences
>g13952.t1 Gene=g13952 Length=1182
ATGGCAGATATAGAAAATAATAACGATTTAACAAAAGATCAAAATGAAGAGAAAGAAGAT
ATTGTGACACCATGGGATGTTGAAGGAGCTAATGATTCAGGAATAGATTATGAGAAACTT
ATTAAGAGATTTGGCAGTTCACGGATTGACGATGCACTTATTGAACGACTAGAAAAAGTG
ATTAAAAAGCCCGTACATCATTTTATCAAAAGAGGAATCTTCTTTTCACATCGAGATCTT
CATACACTTCTCAATCTTTATGAGCAAGGAAAACCTTTTTATCTCTATACAGGAAGAGGT
CCATCGTCAGAATCTATGCATCTTGGTCATTTAATTCCTTTTATTATTACAAAATGGTTA
CAAGAAGCTTTTAATGTACCACTTGTGATTCAAATGTCTGACGATGAAAAAGTTATATGG
AAAGACTTACCTGTAGAAGAGGGTATTAGATTATCAATTGAAAATGCAAGAGATATTATT
GCTATGGGTTTCGATATTGAAAAGACTTTTATTTTTTCAAATTTATGTTATATGGGACAA
TGTCCAGAATATTACAAAAACATTGTGAAAATTGAAAAGTGTGTGACATATAATCAAGTT
AAAGGAATTTTTGGATTTATTGAGGATGATGTGCTAGGAAAAGTTGGATTTCCTGCTGTT
GAGGCTGCACCAGCTTTATCGACATCTTTTCCATTCATTTTTGGTGACAAAAAACGTCAA
GTGTTAATTCCATGTGCTATTGATCAAGACCCATACTTTCGCATGCTTAGAGATGTTGCT
CCACGCCTTGGTTTTGCAAAGCCTGCCCTCTTACATTCAACTTTTTTTCCTGCATTGCAA
GGAGCTAAATCGAAAATGTCAGCGAGCAATTTTAATTCAGCAATTTTCTTAACTGATACT
CAAGAAGAAATTGCCATGAAAATTAACGATCACACCTTCACAGCAGAAGGAAATGTTGAC
ATCGATGTTCCTTACAAACTCCTCACATTCTTTCTTTCTGACGACAATGAATTGGAACGA
GTAAAGAATGCATTCAGTTCTGGTCAAATGTCATCAGCAGAAATTCGAAAAATTGCAATC
GATTGTTTGCAGCCAATTGTTCGTGAGCACCAAGAAAAAAGGAAACTTGTAACGGATGAA
GTTGTCGAACAATATATGACAGTTAGAAAATTGAATTGCTAG
>g13952.t1 Gene=g13952 Length=393
MADIENNNDLTKDQNEEKEDIVTPWDVEGANDSGIDYEKLIKRFGSSRIDDALIERLEKV
IKKPVHHFIKRGIFFSHRDLHTLLNLYEQGKPFYLYTGRGPSSESMHLGHLIPFIITKWL
QEAFNVPLVIQMSDDEKVIWKDLPVEEGIRLSIENARDIIAMGFDIEKTFIFSNLCYMGQ
CPEYYKNIVKIEKCVTYNQVKGIFGFIEDDVLGKVGFPAVEAAPALSTSFPFIFGDKKRQ
VLIPCAIDQDPYFRMLRDVAPRLGFAKPALLHSTFFPALQGAKSKMSASNFNSAIFLTDT
QEEIAMKINDHTFTAEGNVDIDVPYKLLTFFLSDDNELERVKNAFSSGQMSSAEIRKIAI
DCLQPIVREHQEKRKLVTDEVVEQYMTVRKLNC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g13952.t1 | Coils | Coil | Coil | 1 | 21 | - |
| 10 | g13952.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 12 | 288 | 1.6E-123 |
| 9 | g13952.t1 | Gene3D | G3DSA:1.10.240.10 | - | 289 | 393 | 5.9E-33 |
| 13 | g13952.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 14 | g13952.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 9 | 24 | - |
| 2 | g13952.t1 | PANTHER | PTHR10055:SF1 | TRYPTOPHAN–TRNA LIGASE, CYTOPLASMIC | 18 | 392 | 9.7E-166 |
| 3 | g13952.t1 | PANTHER | PTHR10055 | TRYPTOPHANYL-TRNA SYNTHETASE | 18 | 392 | 9.7E-166 |
| 6 | g13952.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 106 | 122 | 6.1E-19 |
| 4 | g13952.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 158 | 177 | 6.1E-19 |
| 5 | g13952.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 241 | 262 | 6.1E-19 |
| 7 | g13952.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 285 | 295 | 6.1E-19 |
| 1 | g13952.t1 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 244 | 375 | 1.1E-9 |
| 12 | g13952.t1 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 101 | 111 | - |
| 8 | g13952.t1 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 20 | 389 | 2.2E-89 |
| 15 | g13952.t1 | TIGRFAM | TIGR00233 | trpS: tryptophan–tRNA ligase | 91 | 387 | 5.9E-74 |
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.
