General information for g3988.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phenylalanine–tRNA ligase alpha subunit.
Parent gene
- The parent gene g3988 is located on chr_3: 29396607..29399724 (+ 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 | g3988 | g3988.t11 | TSS | g3988.t11 | 29394985 | 29394985 |
| chr_3 | g3988 | g3988.t11 | isoform | g3988.t11 | 29395656 | 29396710 |
| chr_3 | g3988 | g3988.t11 | exon | g3988.t11.exon1 | 29395656 | 29396710 |
| chr_3 | g3988 | g3988.t11 | cds | g3988.t11.CDS1 | 29395696 | 29396607 |
| chr_3 | g3988 | g3988.t11 | TTS | g3988.t11 | NA | NA |
Sequences
>g3988.t11 Gene=g3988 Length=1055
AACGACACTTACGAAACTTGAAACAGACTTAACTTCTGACATGCTCACTTCAGGTGCTTG
GAAAAATCTTAAATTCAAGGAATATAATTTCGATGCCCTTGGTGCAGTGCCACAAGCTGG
ATATCAACATCCACTTCTTAAAGTTCGCACCGAAGTATCAGAAATTTTCACTCAAATGGG
ATTTGTTGAAATGCCAACAAATAATTATGTTGAGGCATCTTTCTGGAATTTTGATGCACT
CTTTCAACCACAAATGCATCCTGCTAGAGACGCTCAAGATACATTCTTCCTTTCAATTCC
TGAAAAGAGTTATAAATTTCCCACATCATATCTCGAACGAGTGAAAAATGCTCATGAAAA
TGGTGGTAATGGATCAATCGGTTATAGATACAATTGGAAAATAGAAGAGGCACAAAAAAA
TATTTTAAGAACTCATACTACAGGTGTATCTGCACGAATGCTCTATAAATTAGCAAATCA
AGAAGGTGGATTTAAGCCTGTTAAATATTTTTCAATTGATAAAGTTTTCCGTAATGAAAC
ATTAGATGCTACTCATCTTGCTGAATTCCATCAAGTCGAAGGTGTCATTGCTGGCGTTGA
TATAAGCTTAGGAGGTCTTAAAGGAATAATTTCAGAATTTTTCTCTAAAATGGGTCTCAC
TGATGTGCAGTTCAAACCTGCATATAATCCATATACTGAACCTTCTATGGAAATTTTCGC
ATATCATAAAGGTCTCGGAAAATTGATTGAAATTGGAAATAGTGGAATGTTTAGAAGAGA
AATGTTAGATCCAATGAATATCCCAAGTAATGTAAATGTATATGGATATGGTCTCTCATT
AGAAAGACCTACAATGATAAAATATGGCATTAAAAATATCCGTGAATTAATTGGACCTAA
AGTTGATTTGAAAATGGTGCAAGAATCTGCATTATGTCGCTTAGATAAATAATTTAATTA
TCTTACTGCTCTTATAACGAATAAAAAATTTCTTTTTTGCTTTAAAATATTTTGATCGAA
ATTTTTATTTGCATTAAAGTGCTATTACATTTTCT
>g3988.t11 Gene=g3988 Length=303
MLTSGAWKNLKFKEYNFDALGAVPQAGYQHPLLKVRTEVSEIFTQMGFVEMPTNNYVEAS
FWNFDALFQPQMHPARDAQDTFFLSIPEKSYKFPTSYLERVKNAHENGGNGSIGYRYNWK
IEEAQKNILRTHTTGVSARMLYKLANQEGGFKPVKYFSIDKVFRNETLDATHLAEFHQVE
GVIAGVDISLGGLKGIISEFFSKMGLTDVQFKPAYNPYTEPSMEIFAYHKGLGKLIEIGN
SGMFRREMLDPMNIPSNVNVYGYGLSLERPTMIKYGIKNIRELIGPKVDLKMVQESALCR
LDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3988.t11 | CDD | cd00496 | PheRS_alpha_core | 30 | 289 | 0.000 |
| 5 | g3988.t11 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 1 | 303 | 0.000 |
| 2 | g3988.t11 | PANTHER | PTHR11538 | PHENYLALANYL-TRNA SYNTHETASE | 14 | 302 | 0.000 |
| 3 | g3988.t11 | PANTHER | PTHR11538:SF40 | PHENYLALANINE–TRNA LIGASE ALPHA SUBUNIT | 14 | 302 | 0.000 |
| 1 | g3988.t11 | Pfam | PF01409 | tRNA synthetases class II core domain (F) | 15 | 293 | 0.000 |
| 7 | g3988.t11 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 153 | 286 | 17.161 |
| 4 | g3988.t11 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 15 | 289 | 0.000 |
| 6 | g3988.t11 | TIGRFAM | TIGR00468 | pheS: phenylalanine–tRNA ligase, alpha subunit | 3 | 289 | 0.000 |
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:0006432 | phenylalanyl-tRNA aminoacylation | BP |
| GO:0005524 | ATP binding | MF |
| GO:0000049 | tRNA binding | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0004826 | phenylalanine-tRNA ligase activity | MF |
| GO:0000166 | nucleotide binding | MF |
| GO:0043039 | tRNA aminoacylation | BP |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01889 (phenylalanyl-tRNA synthetase alpha chain)
Pathway
- This transcript belongs to the following pathways
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.
