General information for g3578.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Valine–tRNA ligase.
Parent gene
- The parent gene g3578 is located on chr_3: 26527032..26528478 (+ 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 | g3578 | g3578.t23 | isoform | g3578.t23 | 26527032 | 26527559 |
| chr_3 | g3578 | g3578.t23 | exon | g3578.t23.exon1 | 26527032 | 26527559 |
| chr_3 | g3578 | g3578.t23 | cds | g3578.t23.CDS1 | 26527133 | 26527558 |
| chr_3 | g3578 | g3578.t23 | TTS | g3578.t23 | 26528550 | 26528550 |
| chr_3 | g3578 | g3578.t23 | TSS | g3578.t23 | NA | NA |
Sequences
>g3578.t23 Gene=g3578 Length=528
CTGTATTTGGCTGGCCTGATCAAACAGAAGATTTGAAACTTTTTTATCCAACGACTCTTC
TCGAAACAGGTCATGATATTTTATTTTTTTGGGTAGCTCGTATGGTTTTCTTTGGTCAAA
CTTTATTAGGTAAACTTCCATTTAAGTATGTTTTTCTTCATCCTATGGTTCGCGATGCGC
ATGGAAGAAAAATGTCAAAATCGCTTGGAAATGTTATTGATCCTATGGACGTTATAAACG
GAATCTCGCTCGATGGATTGCATCAACAATTAATAGATTCAAATTTAGATCCTCGTGAAA
TTGAAAAAGCAAAAGCAGGTCAAAAACAAGATTTTCCAAACGGTATTCCTGAATGTGGAA
CAGATGCTATGCGATTTACACTTTGTAATTACATGACTCAAGCAAGAGATATTAATTTAG
ATATCATGCGTGTACAAGGCTATAGATTTTTCTGCAATAAGCTGTGGAATGCTACGAAAT
TTGCATTAAGATATTTTGAAGATGGTGAAACATATGAAATTCATGATA
>g3578.t23 Gene=g3578 Length=142
MVFFGQTLLGKLPFKYVFLHPMVRDAHGRKMSKSLGNVIDPMDVINGISLDGLHQQLIDS
NLDPREIEKAKAGQKQDFPNGIPECGTDAMRFTLCNYMTQARDINLDIMRVQGYRFFCNK
LWNATKFALRYFEDGETYEIHD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3578.t23 | Gene3D | G3DSA:3.40.50.620 | HUPs | 14 | 54 | 6e-07 |
| 6 | g3578.t23 | Gene3D | G3DSA:1.10.730.10 | - | 58 | 141 | 0e+00 |
| 2 | g3578.t23 | PANTHER | PTHR11946:SF110 | VALINE–TRNA LIGASE | 1 | 134 | 0e+00 |
| 3 | g3578.t23 | PANTHER | PTHR11946 | VALYL-TRNA SYNTHETASES | 1 | 134 | 0e+00 |
| 1 | g3578.t23 | Pfam | PF00133 | tRNA synthetases class I (I, L, M and V) | 1 | 107 | 0e+00 |
| 4 | g3578.t23 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 2 | 114 | 0e+00 |
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: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.
