General information for g13952.t4
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.t4 | TSS | g13952.t4 | 33574101 | 33574101 |
| chr_1 | g13952 | g13952.t4 | isoform | g13952.t4 | 33574165 | 33575608 |
| chr_1 | g13952 | g13952.t4 | exon | g13952.t4.exon1 | 33574165 | 33574669 |
| chr_1 | g13952 | g13952.t4 | cds | g13952.t4.CDS1 | 33574632 | 33574669 |
| chr_1 | g13952 | g13952.t4 | exon | g13952.t4.exon2 | 33574727 | 33574909 |
| chr_1 | g13952 | g13952.t4 | cds | g13952.t4.CDS2 | 33574727 | 33574909 |
| chr_1 | g13952 | g13952.t4 | exon | g13952.t4.exon3 | 33574963 | 33575608 |
| chr_1 | g13952 | g13952.t4 | cds | g13952.t4.CDS3 | 33574963 | 33575608 |
| chr_1 | g13952 | g13952.t4 | TTS | g13952.t4 | 33575671 | 33575671 |
Sequences
>g13952.t4 Gene=g13952 Length=1334
ATGGCAGATATAGAAAATAATAACGATTTAACAAAAGATCAAAATGAAGAGAAAGAAGAT
ATTGTGACACCATGGGATGTTGAAGGTAAAAAATGAAAATTCCACTGATGAAATATCAGT
GAAATATTTCACTCGAAAAAATATTGCAAAATAATTTTAAGATATTTTAACTTAATTGCT
CTAATTTGCCATTGAATTTTAATGATATATATTTTTCGTTTATTTATTAAAAATCAGGAG
CTAATGATTCAGGAATAGATTATGAGAAACTTATTAAGAGATTTGGCAGTTCACGGATTG
ACGATGCACTTATTGAACGACTAGAAAAAGTGATTAAAAAGCCCGTACATCATTTTATCA
AAAGAGGAATCTTCTTTTCACATCGAGATCTTCATACACTTCTCAATCTTTATGAGCAAG
GAAAACCTTTTTATCTCTATACAGGAAGAGGTCCATCGTCAGAATCTATGCATCTTGGTC
ATTTAATTCCTTTTATTATTACAAAATGGTTACAAGAAGCTTTTAATGTACCACTTGTGA
TTCAAATGTCTGACGATGAAAAAGTTATATGGAAAGACTTACCTGTAGAAGAGGGTATTA
GATTATCAATTGAAAATGCAAGAGATATTATTGCTATGGGTTTCGATATTGAAAAGACTT
TTATTTTTTCAAATTTATGTTATATGGGACAATGTCCAGAATATTACAAAAACATTGTGA
AAATTGAAAAGTGTGTGACATATAATCAAGTTAAAGGAATTTTTGGATTTATTGAGGATG
ATGTGCTAGGAAAAGTTGGATTTCCTGCTGTTGAGGCTGCACCAGCTTTATCGACATCTT
TTCCATTCATTTTTGGTGACAAAAAACGTCAAGTGTTAATTCCATGTGCTATTGATCAAG
ACCCATACTTTCGCATGCTTAGAGATGTTGCTCCACGCCTTGGTTTTGCAAAGCCTGCCC
TCTTACATTCAACTTTTTTTCCTGCATTGCAAGGAGCTAAATCGAAAATGTCAGCGAGCA
ATTTTAATTCAGCAATTTTCTTAACTGATACTCAAGAAGAAATTGCCATGAAAATTAACG
ATCACACCTTCACAGCAGAAGGAAATGTTGACATCGATGTTCCTTACAAACTCCTCACAT
TCTTTCTTTCTGACGACAATGAATTGGAACGAGTAAAGAATGCATTCAGTTCTGGTCAAA
TGTCATCAGCAGAAATTCGAAAAATTGCAATCGATTGTTTGCAGCCAATTGTTCGTGAGC
ACCAAGAAAAAAGGAAACTTGTAACGGATGAAGTTGTCGAACAATATATGACAGTTAGAA
AATTGAATTGCTAG
>g13952.t4 Gene=g13952 Length=288
MHLGHLIPFIITKWLQEAFNVPLVIQMSDDEKVIWKDLPVEEGIRLSIENARDIIAMGFD
IEKTFIFSNLCYMGQCPEYYKNIVKIEKCVTYNQVKGIFGFIEDDVLGKVGFPAVEAAPA
LSTSFPFIFGDKKRQVLIPCAIDQDPYFRMLRDVAPRLGFAKPALLHSTFFPALQGAKSK
MSASNFNSAIFLTDTQEEIAMKINDHTFTAEGNVDIDVPYKLLTFFLSDDNELERVKNAF
SSGQMSSAEIRKIAIDCLQPIVREHQEKRKLVTDEVVEQYMTVRKLNC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13952.t4 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 184 | 0 |
| 9 | g13952.t4 | Gene3D | G3DSA:1.10.240.10 | - | 185 | 288 | 0 |
| 2 | g13952.t4 | PANTHER | PTHR10055:SF1 | TRYPTOPHAN–TRNA LIGASE, CYTOPLASMIC | 1 | 287 | 0 |
| 3 | g13952.t4 | PANTHER | PTHR10055 | TRYPTOPHANYL-TRNA SYNTHETASE | 1 | 287 | 0 |
| 7 | g13952.t4 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 1 | 17 | 0 |
| 5 | g13952.t4 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 53 | 72 | 0 |
| 4 | g13952.t4 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 136 | 157 | 0 |
| 6 | g13952.t4 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 180 | 190 | 0 |
| 1 | g13952.t4 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 139 | 270 | 0 |
| 8 | g13952.t4 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 1 | 284 | 0 |
| 11 | g13952.t4 | TIGRFAM | TIGR00233 | trpS: tryptophan–tRNA ligase | 1 | 282 | 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.
