General information for g5883.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alanine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g5883 is located on chr_2: 12576087..12578032 (+ 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_2 | g5883 | g5883.t3 | TSS | g5883.t3 | 12574792 | 12574792 |
| chr_2 | g5883 | g5883.t3 | isoform | g5883.t3 | 12574876 | 12575551 |
| chr_2 | g5883 | g5883.t3 | exon | g5883.t3.exon1 | 12574876 | 12574934 |
| chr_2 | g5883 | g5883.t3 | exon | g5883.t3.exon2 | 12575058 | 12575551 |
| chr_2 | g5883 | g5883.t3 | cds | g5883.t3.CDS1 | 12575064 | 12575549 |
| chr_2 | g5883 | g5883.t3 | TTS | g5883.t3 | NA | NA |
Sequences
>g5883.t3 Gene=g5883 Length=553
TGAAATTAATAGATATTACCTCATCAGTGCATAAGATATAATATTCCAGTGAAATTAAGG
AAAAAATGGATACCACGCTGACAGCAAATCAAATTCGTAAGCTCTTTTTGGATTTCTTTG
AAGAGCAAAAACATATTTATGTTCATTCATCATCAACAATTCCTCTCGATGATCCAACAT
TGCTCTTTGCAAATGCTGGAATGAATCAATTCAAGCCAATTTTCTTGGGAACTGCCGATC
CAAATTCTGAAATGTCAAAATGGGTAAGAGTTGCAAACACTCAAAAGTGCATTCGTGCTG
GAGGCAAGCACAACGATTTAGATGATGTTGGAAAAGATGTTTATCATCACACTTTCTTTG
AAATGCTTGGCAACTGGTCATTTGGTGACTATTTCAAAAAAGAAATCTGTACATGGGCTT
GGGAATTCTTGACTGGTCGCCTTAAACTGCCAAAAGATCGACTCTATGTAACATATTTTG
GTGGTGATAAAGATGCCGGCTTAGAACCAGATTTGGAATGCAAACAAATCTGGACAGATT
TGGGAGTTTTACC
>g5883.t3 Gene=g5883 Length=162
MDTTLTANQIRKLFLDFFEEQKHIYVHSSSTIPLDDPTLLFANAGMNQFKPIFLGTADPN
SEMSKWVRVANTQKCIRAGGKHNDLDDVGKDVYHHTFFEMLGNWSFGDYFKKEICTWAWE
FLTGRLKLPKDRLYVTYFGGDKDAGLEPDLECKQIWTDLGVL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5883.t3 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 4 | 162 | 0.000 |
| 2 | g5883.t3 | PANTHER | PTHR11777:SF8 | ALANINE–TRNA LIGASE, MITOCHONDRIAL | 3 | 161 | 0.000 |
| 3 | g5883.t3 | PANTHER | PTHR11777 | ALANYL-TRNA SYNTHETASE | 3 | 161 | 0.000 |
| 1 | g5883.t3 | Pfam | PF01411 | tRNA synthetases class II (A) | 9 | 160 | 0.000 |
| 6 | g5883.t3 | ProSiteProfiles | PS50860 | Alanyl-transfer RNA synthetases family profile. | 5 | 162 | 30.869 |
| 4 | g5883.t3 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 5 | 144 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5883/g5883.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5883.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0000166 | nucleotide binding | MF |
| GO:0006419 | alanyl-tRNA aminoacylation | BP |
| GO:0004813 | alanine-tRNA ligase activity | MF |
| GO:0003676 | nucleic acid binding | 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.
