General information for g3833.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bifunctional glutamate/proline–tRNA ligase.
Parent gene
- The parent gene g3833 is located on chr_3: 28290022..28291097 (+ 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 | g3833 | g3833.t9 | isoform | g3833.t9 | 28288680 | 28289411 |
| chr_3 | g3833 | g3833.t9 | exon | g3833.t9.exon1 | 28288680 | 28289411 |
| chr_3 | g3833 | g3833.t9 | cds | g3833.t9.CDS1 | 28288688 | 28289410 |
| chr_3 | g3833 | g3833.t9 | TTS | g3833.t9 | 28289455 | 28289455 |
| chr_3 | g3833 | g3833.t9 | TSS | g3833.t9 | NA | NA |
Sequences
>g3833.t9 Gene=g3833 Length=732
GTCGTGGTATGACTGTTGAAGGTTTAAAACAATTCATTATTGCACAAGGTTCTAGTAAAG
CTGTTGTATTTATGGAATGGGATAAAATTTGGGCTTTCAACAAAAAAGTCATCGATCCAA
TTGCACCTAGATACATTGCATTAGAAAACGACAATCGTATAATTGTCAAAGTTAATAATG
CAATATTACAAGCTCTTGAAGTTCCAAGACATCCCAAAAATAATGAAGTTGGCACAAAAA
CTATTTGGGTTGGCCCAGAAATTTATATTGACTATGCTGATGCTGAATCCTTAAAAGAAG
GTGAAAATGCAACATTTATAAATTGGGGTAATTTAAGAATCAAAAAGATTCATAAAGAAA
GTGAAAAAATTACTTCTATCGATGCTGAATTGAATTTGAGTGATACCGATTTCAAAAAGA
CATTAAAACTGACATGGCTTTGTAAACAGGATCCTTCAGAATATCCAACAACTTATTGCG
TTTATTTCGATCATATAATTAGCAAAGCTGTTCTTGGTAAAAATGAAGACTTTAAAGCAT
ATATCGGACATGAGACTAGAAAAGAAACAAAAATGTTGGCTGATCCTGAATTGAAAAAAT
GTCAGAAAGGCGATATCATTCAACTACAACGGCGCGGATTTTTCAAAGTTGATCAAGCTT
ATGCTCCAGCTAGCGAAATTTCAGGATCAGAACGTCCAATTGTATTGTACTTTATTCCTG
ATGGTCACAAAA
>g3833.t9 Gene=g3833 Length=241
MTVEGLKQFIIAQGSSKAVVFMEWDKIWAFNKKVIDPIAPRYIALENDNRIIVKVNNAIL
QALEVPRHPKNNEVGTKTIWVGPEIYIDYADAESLKEGENATFINWGNLRIKKIHKESEK
ITSIDAELNLSDTDFKKTLKLTWLCKQDPSEYPTTYCVYFDHIISKAVLGKNEDFKAYIG
HETRKETKMLADPELKKCQKGDIIQLQRRGFFKVDQAYAPASEISGSERPIVLYFIPDGH
K
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g3833.t9 | Gene3D | G3DSA:2.40.240.10 | Ribosomal Protein L25; Chain P | 40 | 218 | 0 |
| 5 | g3833.t9 | Gene3D | G3DSA:2.40.240.10 | Ribosomal Protein L25; Chain P | 47 | 149 | 0 |
| 2 | g3833.t9 | PANTHER | PTHR43382 | PROLYL-TRNA SYNTHETASE | 1 | 241 | 0 |
| 1 | g3833.t9 | Pfam | PF03950 | tRNA synthetases class I (E and Q), anti-codon binding domain | 39 | 215 | 0 |
| 3 | g3833.t9 | SUPERFAMILY | SSF50715 | Ribosomal protein L25-like | 39 | 240 | 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:0006412 | translation | BP |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
| GO:0005737 | cytoplasm | CC |
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.
