General information for g3988.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t10 | TSS | g3988.t10 | 29394985 | 29394985 |
| chr_3 | g3988 | g3988.t10 | isoform | g3988.t10 | 29395061 | 29395769 |
| chr_3 | g3988 | g3988.t10 | exon | g3988.t10.exon1 | 29395061 | 29395346 |
| chr_3 | g3988 | g3988.t10 | cds | g3988.t10.CDS1 | 29395061 | 29395346 |
| chr_3 | g3988 | g3988.t10 | exon | g3988.t10.exon2 | 29395399 | 29395769 |
| chr_3 | g3988 | g3988.t10 | cds | g3988.t10.CDS2 | 29395399 | 29395460 |
| chr_3 | g3988 | g3988.t10 | TTS | g3988.t10 | 29396662 | 29396662 |
Sequences
>g3988.t10 Gene=g3988 Length=657
ATGCAGCTAGAGTTGACCGAACAAATTCTTCATTTCATTGAGCATCATAAGAAAGCTGAT
TCAATTGATTTAGCAGCTGAATTCAAAGAAGATCATCAAAAAGTAATTGGAGCATTAAAA
AGTATCGAAGCTCATGGTGAAATTTTAAAGTCTGAGACTACAACAAAAAAAGTTTGGGAT
CTAACTAATGAAGGACATTATGTCATAGAGCATGGATCACATGAAGCTACTGTTTTTAAT
GCTATTCCCAATGCAGGAATTTTGCAAGCCGATTTGATGAAAGTAGACATCACCAAATGC
AAAAGTAGGATTTTCAAAAGCAATGAATGCAGGATGGATTGTTATTGACAAATCGGGCAA
AACTCCTTTAGTAAAAAGAAAAGTCGAATCGATTGATGATGTTGTGCAACAGCATTTAAT
TGAAATTCAAAGTGGAAAAAGTACAAACATTCCTGATAACATCAAAGCTGATTATAAGAA
ACGAAAACTTTTAGTTGAAAATACTATTAAAAGTTTTATTATTACAAAGGGTCCTGAATT
TACAACGACACTTACGAAACTTGAAACAGACTTAACTTCTGACATGCTCACTTCAGGTGC
TTGGAAAAATCTTAAATTCAAGGAATATAATTTCGATGCCCTTGGTGCAGTGCCACA
>g3988.t10 Gene=g3988 Length=115
MQLELTEQILHFIEHHKKADSIDLAAEFKEDHQKVIGALKSIEAHGEILKSETTTKKVWD
LTNEGHYVIEHGSHEATVFNAIPNAGILQADLMKVDITKCKSRIFKSNECRMDCY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g3988.t10 | Gene3D | G3DSA:1.10.10.2310 | - | 1 | 77 | 0.0e+00 |
| 5 | g3988.t10 | Gene3D | G3DSA:1.10.10.2330 | - | 78 | 100 | 6.9e-06 |
| 2 | g3988.t10 | PANTHER | PTHR11538 | PHENYLALANYL-TRNA SYNTHETASE | 6 | 100 | 0.0e+00 |
| 3 | g3988.t10 | PANTHER | PTHR11538:SF40 | PHENYLALANINE–TRNA LIGASE ALPHA SUBUNIT | 6 | 100 | 0.0e+00 |
| 1 | g3988.t10 | Pfam | PF18552 | PheRS DNA binding domain 1 | 1 | 59 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
