General information for g4655.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Leucine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g4655 is located on chr_2: 3964597..3965678 (- 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 | g4655 | g4655.t2 | TTS | g4655.t2 | 3961787 | 3961787 |
| chr_2 | g4655 | g4655.t2 | isoform | g4655.t2 | 3961872 | 3963117 |
| chr_2 | g4655 | g4655.t2 | exon | g4655.t2.exon1 | 3961872 | 3962522 |
| chr_2 | g4655 | g4655.t2 | cds | g4655.t2.CDS1 | 3961872 | 3962522 |
| chr_2 | g4655 | g4655.t2 | exon | g4655.t2.exon2 | 3962581 | 3963117 |
| chr_2 | g4655 | g4655.t2 | cds | g4655.t2.CDS2 | 3962581 | 3963111 |
| chr_2 | g4655 | g4655.t2 | TSS | g4655.t2 | NA | NA |
Sequences
>g4655.t2 Gene=g4655 Length=1188
AAAGAAATGATTGCTGGAAAACTTTTATTGAGAACTGGTTCAAAAGATGCTTTTTATGAT
CGTGTTTTCATTAGTGAAATGAATAGTTTCATTAAACAAACTGATGAGAACTATAACAAA
ATGCTTTACAAAGAAGCATTGAGAACAGGTGTTTTCGAATTTCAACGTGCAAGAGATACT
TATCGTGAACTTTGTGGTGCAAACAACATGCATGTTGATTTAGTTTTTCAATTTATCGAA
AATCAAGCACTTTTAATGGCACCAATTTGTCCGCATGTTGCTGAACATATTTGGGGCTTG
TTAGGAAAATCAGGAAGCATTGTAAATGCCAAATTCCCTGTAGCTGGACCAATTGATGAG
AAACTTATCAAATGTTCTGATTATCTGATGGAAGCAGCTCACAATTTCCGCTTACTCTAC
AAAAAAAACTTTTCAGCTAAAGGTGCACAAAAACCAACGGGTGCAACTATCTGGATTGCT
AAAACTTTTCCACCATGGCAGAGTTGTGTAATTGATACAATGAGAAATCTTTATGAGAAA
AATAATTCTGTTCTTCCGGATAATAAACTTGTTAGTGCTGAGTTAATGAAAATAGAATCG
CTCAAAAAATATCAGAAGAAAGCAATGCCATTTGTGCAGAGAATTAGAGATCGTGTGAGT
GTTTTGGGAAAATCAGCAATGGCAGTTACTGTCGATTTTGATGAGCATGGAGTTATTGAA
ACAAATTTACAGTACTTGAAAGGAACACTCGATTTGGAGCAAATTGAAATTCGATTCACT
GATGATCCATCAGCAACTGAAAATACAAGAGAGAGTGTACAACCAGGAAGTCCTTTCATT
TCTTATATTGTAAAGCCATCAGTTAGAGTAAATTTTGAGAACCCAATCCCACGTTCGGGC
CTTTTTACTCAGCAAATAAACGTGGGAGAAGGTGACACTTTAAATACACTAAAAGAAAAG
CTCGCTAAAGGATTAGGACTTAAAGTCACGACAGCAATTCAATTATGGAGATTTGAAGAT
CATGTTTTAGGGCCAAGAAAAATGCCAATTTTTAATGATTTTAAGACAGGAAAGAAACAG
ATAGAAGAAGGAATATTCTCAGTTGATGCTAAAGATTCAAAAGTTTTCATCACAAATAAT
GAAAGTAAAATCGAAGTTGGAACAAATTTCATCTATGTTGTTGAATGA
>g4655.t2 Gene=g4655 Length=393
MIAGKLLLRTGSKDAFYDRVFISEMNSFIKQTDENYNKMLYKEALRTGVFEFQRARDTYR
ELCGANNMHVDLVFQFIENQALLMAPICPHVAEHIWGLLGKSGSIVNAKFPVAGPIDEKL
IKCSDYLMEAAHNFRLLYKKNFSAKGAQKPTGATIWIAKTFPPWQSCVIDTMRNLYEKNN
SVLPDNKLVSAELMKIESLKKYQKKAMPFVQRIRDRVSVLGKSAMAVTVDFDEHGVIETN
LQYLKGTLDLEQIEIRFTDDPSATENTRESVQPGSPFISYIVKPSVRVNFENPIPRSGLF
TQQINVGEGDTLNTLKEKLAKGLGLKVTTAIQLWRFEDHVLGPRKMPIFNDFKTGKKQIE
EGIFSVDAKDSKVFITNNESKIEVGTNFIYVVE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4655.t2 | CDD | cd07959 | Anticodon_Ia_Leu_AEc | 16 | 99 | 0 |
| 5 | g4655.t2 | Gene3D | G3DSA:1.10.730.10 | - | 8 | 100 | 0 |
| 2 | g4655.t2 | PANTHER | PTHR45794 | LEUCYL-TRNA SYNTHETASE | 8 | 280 | 0 |
| 3 | g4655.t2 | PANTHER | PTHR45794:SF1 | LEUCINE–TRNA LIGASE, CYTOPLASMIC | 8 | 280 | 0 |
| 1 | g4655.t2 | Pfam | PF08264 | Anticodon-binding domain of tRNA ligase | 18 | 135 | 0 |
| 4 | g4655.t2 | SUPERFAMILY | SSF47323 | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 15 | 204 | 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:0004823 | leucine-tRNA ligase activity | MF |
| GO:0005524 | ATP binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0006429 | leucyl-tRNA aminoacylation | BP |
| 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.
