General information for g1213.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tyrosine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g1213 is located on chr_3: 8799190..8800645 (+ 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 | g1213 | g1213.t3 | TSS | g1213.t3 | 8797313 | 8797313 |
| chr_3 | g1213 | g1213.t3 | isoform | g1213.t3 | 8797434 | 8798185 |
| chr_3 | g1213 | g1213.t3 | exon | g1213.t3.exon1 | 8797434 | 8797637 |
| chr_3 | g1213 | g1213.t3 | cds | g1213.t3.CDS1 | 8797434 | 8797637 |
| chr_3 | g1213 | g1213.t3 | exon | g1213.t3.exon2 | 8797711 | 8798185 |
| chr_3 | g1213 | g1213.t3 | cds | g1213.t3.CDS2 | 8797711 | 8798184 |
| chr_3 | g1213 | g1213.t3 | TTS | g1213.t3 | NA | NA |
Sequences
>g1213.t3 Gene=g1213 Length=679
ATGGCAGAAGAATTGACATTTGAAAAGAAACTTGAGTTAATCAAAAGAAATCTGCAAGAG
GTTCTTGGTGAAGAAAATCTGCACAAGATTGTGAAAGAACGAGATTTAAAACTTTATTGG
GGAACTGCCACAACTGGAAAACCTCATATTGCATATTTCGTGCCAATGACAAAAATTGCA
GACTTTCTAAAAGCTGGATGTGAAGTCACAATCTTGTTTGCAGACTTACATGCATATTTA
GATAATATGAAAGCACCATGGTCACTTCTAGAAGAGAGAACAAAATATTATGAAGCTGTT
ATTAAAGCTATGCTTCAATCACTAGGTGTACCATTGGAGAAACTTAAATTCGTGCAAGGC
ACAAGTTTTGAATTGTCTCGTGAATACTCTTTAGATGTTTATAGACTCACATCAATTGTG
ACTCAACATGATGCTAAAAAAGCTGGTGCTGAAGTTGTGAAACAAGTTGAATATCCTCTT
TTATCTGGATTGCTTTATCCTGGCCTTCAGGCACTCGATGAAGAATATTTAAAAGTTGAT
GCTCAATTTGGAGGTGTTGATCAAAGAAAAATTTTTACTTTTGCTGAAAAATATCTTCCA
CAACTCGGTTATGCAAAGAGAATTCATCTTATGAATCCCATGGTGCCTGGTTTAACAGGT
GGCAAAATGTCTTCTTCTG
>g1213.t3 Gene=g1213 Length=226
MAEELTFEKKLELIKRNLQEVLGEENLHKIVKERDLKLYWGTATTGKPHIAYFVPMTKIA
DFLKAGCEVTILFADLHAYLDNMKAPWSLLEERTKYYEAVIKAMLQSLGVPLEKLKFVQG
TSFELSREYSLDVYRLTSIVTQHDAKKAGAEVVKQVEYPLLSGLLYPGLQALDEEYLKVD
AQFGGVDQRKIFTFAEKYLPQLGYAKRIHLMNPMVPGLTGGKMSSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1213.t3 | Gene3D | G3DSA:3.40.50.620 | HUPs | 5 | 215 | 0 |
| 2 | g1213.t3 | PANTHER | PTHR42765 | SOLEUCYL-TRNA SYNTHETASE | 5 | 226 | 0 |
| 3 | g1213.t3 | PANTHER | PTHR42765:SF2 | TYROSINE–TRNA LIGASE | 5 | 226 | 0 |
| 11 | g1213.t3 | PIRSF | PIRSF006588 | TyrRS_arch_euk | 5 | 226 | 0 |
| 6 | g1213.t3 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 47 | 69 | 0 |
| 5 | g1213.t3 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 158 | 173 | 0 |
| 4 | g1213.t3 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 175 | 197 | 0 |
| 7 | g1213.t3 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 208 | 220 | 0 |
| 1 | g1213.t3 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 33 | 226 | 0 |
| 8 | g1213.t3 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 7 | 226 | 0 |
| 10 | g1213.t3 | TIGRFAM | TIGR00234 | tyrS: tyrosine–tRNA ligase | 10 | 225 | 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:0005524 | ATP binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004831 | tyrosine-tRNA ligase activity | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
| GO:0006437 | tyrosyl-tRNA aminoacylation | BP |
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.
