General information for g2399.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable glutamine–tRNA ligase.
Parent gene
- The parent gene g2399 is located on chr_3: 17638780..17639608 (- 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 | g2399 | g2399.t3 | isoform | g2399.t3 | 17638780 | 17639608 |
| chr_3 | g2399 | g2399.t3 | exon | g2399.t3.exon1 | 17638780 | 17639608 |
| chr_3 | g2399 | g2399.t3 | cds | g2399.t3.CDS1 | 17639134 | 17639502 |
| chr_3 | g2399 | g2399.t3 | TSS | g2399.t3 | 17640433 | 17640433 |
| chr_3 | g2399 | g2399.t3 | TTS | g2399.t3 | NA | NA |
Sequences
>g2399.t3 Gene=g2399 Length=829
AATGTAAGCATTAAAAAGTCTGCAATGAATAAATTGGCATTTAAAATTCAATTAATAAAA
TTATTTGGTAATTTAATTTGTGTACTTTCTTTAATTTTAACAGAAAATGGATGAAGCAAC
TTTTATTTCTAAATTTATTGCACTTGGTTTTAATGAGCAAAAAGCAAAGGAGACTTTAAA
GAATGCAACTCTAACAAAGAATATTACAGCAGCATTTAATTCATTAGATAATCATAATAA
GAAAATTGAAGAATTGACAAAAGGATCTGGAGCATTAGTCTATCATTTATGCTCAAAAAT
CAAGCCTCAATCGCTTCAATATTTAGATCTTCTTATATCTCTCATCACTGAGAATAAGTT
GGATAATAATCTTCGAGTTGATTTAGCATTAGAATTTGTACTTTCACATAGTGTCAGTAA
TACAACAATCAACGTGGCAGATCTTGAAAAGCATTGTGGAGTGAATGTAAGATGAAATAT
GATATAGATTGTATTGTTATTTTTATACTTTCAATTTTAGGTTGTTGTAACACCTGAAGA
AATTGAAGAAGTAGTTGCTGAAGTAATAAAAAAGAACAAGAAAGAGCTCGAAGAACAACG
TTATCGCTTCAATACCGGCAAAATGCTTGCAGAAATTCGTTCAAAAATTCCTTTTGCCGA
TGGAAAAGCTATCAAGTCAGAAGTTGATTGCCAGATATTTTATCTTCTTGGTGCAAAAAC
TGAAGCTGACTTGGCTCCACAGCCAAAGAAGAAGGCAGCTCCATCAAATAATACTGCAAC
TTCAAAATCCGTCAAGCCAAAAGAAGAAGAGGAAGTTTCAAATGATGAC
>g2399.t3 Gene=g2399 Length=122
MDEATFISKFIALGFNEQKAKETLKNATLTKNITAAFNSLDNHNKKIEELTKGSGALVYH
LCSKIKPQSLQYLDLLISLITENKLDNNLRVDLALEFVLSHSVSNTTINVADLEKHCGVN
VR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g2399.t3 | Gene3D | G3DSA:1.10.8.1290 | - | 1 | 121 | 0 |
| 1 | g2399.t3 | Pfam | PF04558 | Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 | 6 | 121 | 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: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.
