General information for g5883.t4
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.t4 | TSS | g5883.t4 | 12574792 | 12574792 |
| chr_2 | g5883 | g5883.t4 | isoform | g5883.t4 | 12574938 | 12576015 |
| chr_2 | g5883 | g5883.t4 | exon | g5883.t4.exon1 | 12574938 | 12576015 |
| chr_2 | g5883 | g5883.t4 | cds | g5883.t4.CDS1 | 12575064 | 12576014 |
| chr_2 | g5883 | g5883.t4 | TTS | g5883.t4 | NA | NA |
Sequences
>g5883.t4 Gene=g5883 Length=1078
AGATAAAATGAATATAAGTAACTTTTCAATTAAATTGCGAAATTGCCACGAATAACAAAA
AAGTGAAAGTACTTAAAACAGGAATTGTCTCACAATTACTCAATCTTAATCTCATTGTAG
GAAAAAATGGATACCACGCTGACAGCAAATCAAATTCGTAAGCTCTTTTTGGATTTCTTT
GAAGAGCAAAAACATATTTATGTTCATTCATCATCAACAATTCCTCTCGATGATCCAACA
TTGCTCTTTGCAAATGCTGGAATGAATCAATTCAAGCCAATTTTCTTGGGAACTGCCGAT
CCAAATTCTGAAATGTCAAAATGGGTAAGAGTTGCAAACACTCAAAAGTGCATTCGTGCT
GGAGGCAAGCACAACGATTTAGATGATGTTGGAAAAGATGTTTATCATCACACTTTCTTT
GAAATGCTTGGCAACTGGTCATTTGGTGACTATTTCAAAAAAGAAATCTGTACATGGGCT
TGGGAATTCTTGACTGGTCGCCTTAAACTGCCAAAAGATCGACTCTATGTAACATATTTT
GGTGGTGATAAAGATGCCGGCTTAGAACCAGATTTGGAATGCAAACAAATCTGGACAGAT
TTGGGAGTTTTACCAGCTCACATTTTACCTGGTTCAATGAAAGACAATTTCTGGGAAATG
GGTGAAACAGGACCTTGTGGACCTTGCAGTGAATTACATTTTGATCGAATTGGCGGAAGA
AGCGTGCCAGAGTTAGTAAATATGGATGATCCCGATGTACTTGAAATTTGGAATCTTGTG
TTTATTCAATTTAATCGTGAAGCTGATTCATCACTCAAGTTACTGCCAAAGAAACATATT
GACTGTGGCATGGGCTTTGAACGTCTTGTATCAGTTATTCAAAACAAGAGATCAAATTAT
GATACTGACATATTTGTACCACTTTTTGATGCTATTCAAAAAGGAACTGGAGCTCGTGCT
TACACTGGTAAAGTTGGAGCAGAAGATGTTGATGGAGTTGATATGGCTTATCGTGTACTC
GCTGATCATGCTCGTACAATCACAATTGCATTAGCTGATGGCGGATTTCCTGATAGCA
>g5883.t4 Gene=g5883 Length=317
MDTTLTANQIRKLFLDFFEEQKHIYVHSSSTIPLDDPTLLFANAGMNQFKPIFLGTADPN
SEMSKWVRVANTQKCIRAGGKHNDLDDVGKDVYHHTFFEMLGNWSFGDYFKKEICTWAWE
FLTGRLKLPKDRLYVTYFGGDKDAGLEPDLECKQIWTDLGVLPAHILPGSMKDNFWEMGE
TGPCGPCSELHFDRIGGRSVPELVNMDDPDVLEIWNLVFIQFNREADSSLKLLPKKHIDC
GMGFERLVSVIQNKRSNYDTDIFVPLFDAIQKGTGARAYTGKVGAEDVDGVDMAYRVLAD
HARTITIALADGGFPDS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5883.t4 | CDD | cd00673 | AlaRS_core | 7 | 254 | 0.000 |
| 10 | g5883.t4 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 4 | 255 | 0.000 |
| 2 | g5883.t4 | PANTHER | PTHR11777:SF34 | ALANINE–TRNA LIGASE, CYTOPLASMIC | 1 | 316 | 0.000 |
| 3 | g5883.t4 | PANTHER | PTHR11777 | ALANYL-TRNA SYNTHETASE | 1 | 316 | 0.000 |
| 7 | g5883.t4 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 83 | 94 | 0.000 |
| 5 | g5883.t4 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 212 | 223 | 0.000 |
| 4 | g5883.t4 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 239 | 252 | 0.000 |
| 6 | g5883.t4 | PRINTS | PR00980 | Alanyl-tRNA synthetase signature | 296 | 312 | 0.000 |
| 1 | g5883.t4 | Pfam | PF01411 | tRNA synthetases class II (A) | 9 | 316 | 0.000 |
| 11 | g5883.t4 | ProSiteProfiles | PS50860 | Alanyl-transfer RNA synthetases family profile. | 5 | 317 | 59.899 |
| 8 | g5883.t4 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 6 | 258 | 0.000 |
| 9 | g5883.t4 | SUPERFAMILY | SSF101353 | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 259 | 316 | 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.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5883.t4.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:0005737 | cytoplasm | CC |
| 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.
