General information for g3170.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Isoleucine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g3170 is located on chr_3: 23433643..23436507 (- 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 | g3170 | g3170.t2 | TTS | g3170.t2 | 23431644 | 23431644 |
| chr_3 | g3170 | g3170.t2 | isoform | g3170.t2 | 23432063 | 23432754 |
| chr_3 | g3170 | g3170.t2 | exon | g3170.t2.exon1 | 23432063 | 23432077 |
| chr_3 | g3170 | g3170.t2 | cds | g3170.t2.CDS1 | 23432065 | 23432077 |
| chr_3 | g3170 | g3170.t2 | exon | g3170.t2.exon2 | 23432136 | 23432754 |
| chr_3 | g3170 | g3170.t2 | cds | g3170.t2.CDS2 | 23432136 | 23432722 |
| chr_3 | g3170 | g3170.t2 | TSS | g3170.t2 | 23433686 | 23433686 |
Sequences
>g3170.t2 Gene=g3170 Length=634
AAGAGAAAGCAACTGGTGCTATTTATATTATCATGGAATCACGTATTGAATATGTTTTCA
AAACAGCTGATGCAGTTGAAGTTTTAGAGAAATTTCCTGGAAAAAATCTTAAAGGACTTT
GTTATGAGCCACCATTTGATTACTTCAAAAAATATAAAGACACAGCTTTTCGTGTATTGT
GCGACAATTATGTGACAGAAGGTTCAGGTTCTGGAGTTGTTCATCAAGCTCCATACTTTG
GTGAAGACGATTATCGGGTTTGCTTGGAAAATAATGTTGTTAAACGTGATCAAGAAATAA
TTTGTCCACTCGATCCTAATGGAAGATTTACAAAAGAAGTTACTGATTTTGTTGGTCAAT
ATGTAAAAGATGCCGATAAAAATATCATGAAACTATTGAAGGAAAAAGGACGTTTAGTTC
GCTCTGGTCAGCATATGCACAGTTATCCATTCTGCTGGCGTTCAGATACACCATTGATTT
ATAAAGCTGTTCCATCATGGTTTGTTCGTGTTGAACATATGACAAAACAATTGCTCGCTA
GTTGTGCTCAAACTTATTGGGTTCCTGATAATGTTAAAGAAAAACGATTTGGTAATTGGC
TCAAAGAAGCAAGAGATTGGGCTATAAGTCGTAA
>g3170.t2 Gene=g3170 Length=200
MESRIEYVFKTADAVEVLEKFPGKNLKGLCYEPPFDYFKKYKDTAFRVLCDNYVTEGSGS
GVVHQAPYFGEDDYRVCLENNVVKRDQEIICPLDPNGRFTKEVTDFVGQYVKDADKNIMK
LLKEKGRLVRSGQHMHSYPFCWRSDTPLIYKAVPSWFVRVEHMTKQLLASCAQTYWVPDN
VKEKRFGNWLKEARDWAISR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3170.t2 | Gene3D | G3DSA:3.90.740.10 | - | 1 | 143 | 0 |
| 2 | g3170.t2 | PANTHER | PTHR42780:SF1 | ISOLEUCINE–TRNA LIGASE, CYTOPLASMIC | 1 | 200 | 0 |
| 3 | g3170.t2 | PANTHER | PTHR42780 | SOLEUCYL-TRNA SYNTHETASE | 1 | 200 | 0 |
| 1 | g3170.t2 | Pfam | PF00133 | tRNA synthetases class I (I, L, M and V) | 1 | 200 | 0 |
| 5 | g3170.t2 | SUPERFAMILY | SSF50677 | ValRS/IleRS/LeuRS editing domain | 3 | 138 | 0 |
| 4 | g3170.t2 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 138 | 200 | 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:0002161 | aminoacyl-tRNA editing activity | 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.
