General information for g12558.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 4-coumarate–CoA ligase-like 2.
Parent gene
- The parent gene g12558 is located on chr_1: 24382099..24383027 (- 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_1 | g12558 | g12558.t3 | isoform | g12558.t3 | 24380754 | 24381570 |
| chr_1 | g12558 | g12558.t3 | exon | g12558.t3.exon1 | 24380754 | 24381510 |
| chr_1 | g12558 | g12558.t3 | TTS | g12558.t3 | 24380785 | 24380785 |
| chr_1 | g12558 | g12558.t3 | cds | g12558.t3.CDS1 | 24381211 | 24381510 |
| chr_1 | g12558 | g12558.t3 | exon | g12558.t3.exon2 | 24381568 | 24381570 |
| chr_1 | g12558 | g12558.t3 | cds | g12558.t3.CDS2 | 24381568 | 24381570 |
| chr_1 | g12558 | g12558.t3 | TSS | g12558.t3 | 24382135 | 24382135 |
Sequences
>g12558.t3 Gene=g12558 Length=760
CAGGTGCCACCTGCTGAAATTGAAAGCATTTTATTAACGCATCCAAAAATCAAAGATGCA
GCAGTTATTGGCATTCCAGATGAGAGAACAGGAGAAAAAGCATTGGCATATGTCGTAAAA
GCTGATGATACATTGACAGAAAAAGAAGTTATTGATTTTATTGCAAAACAAACATCGCCT
GCAAAGCAACTTCATGGTGGATGCATTTTTATCGAACTCATTCCAAAGAATCCGAGTGGA
AAAATTCTTCGAAGAGAACTTAGAGATTTGTATAAACAATCACAGTTAAAGTCCAAATTA
TAAACTAACACTTTCATTCCAAAAGAAGAAAAAAGTTATCAAGACTACGTGTGTATTTTA
CTAGTCAAATGGGACAAATTGGTTATAATATTAATAATTTTAGTGAATTGAAGTTGTAGA
GCTTTAAAATGAACTATTGCGCTTTAGTGTGTGTATAAATACTAGCTAAAATTTTTGTGT
GTGTGTATTTTTTATCTTTTATGTTGACGTCTTCATCTGTTGTACAAACATTAGAGTGAA
GGTCAAGATTATTGTTTTTTAATACCAACACACGCTTTAAGACAAACATAACTTTACTTA
TATAGAAAGGTATAGGTGAGAAAACAAAATTTTAATCTTTTATAACAAGAACAATCTTTA
GAAAATTAATGCACGTAGTAGAGAAAAAAAAAATTATGAATAAAATGTGTGAGGAACAGT
ATTGGGTTATTAAAAATAAAATTGACTTTTACTTTGTTTG
>g12558.t3 Gene=g12558 Length=100
QVPPAEIESILLTHPKIKDAAVIGIPDERTGEKALAYVVKADDTLTEKEVIDFIAKQTSP
AKQLHGGCIFIELIPKNPSGKILRRELRDLYKQSQLKSKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12558.t3 | Gene3D | G3DSA:3.30.300.310 | - | 1 | 97 | 0 |
| 2 | g12558.t3 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 1 | 88 | 0 |
| 3 | g12558.t3 | PANTHER | PTHR24096:SF385 | FATTY ACID COA SYNTHETASE FAMILY | 1 | 88 | 0 |
| 1 | g12558.t3 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 6 | 81 | 0 |
| 4 | g12558.t3 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 2 | 93 | 0 |
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.
