General information for g17096.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 4-coumarate–CoA ligase 2.
Parent gene
- The parent gene g17096 is located on chr_4: 12452070..12453906 (+ 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_4 | g17096 | g17096.t3 | TSS | g17096.t3 | 12452030 | 12452030 |
| chr_4 | g17096 | g17096.t3 | isoform | g17096.t3 | 12452070 | 12453906 |
| chr_4 | g17096 | g17096.t3 | exon | g17096.t3.exon1 | 12452070 | 12453134 |
| chr_4 | g17096 | g17096.t3 | cds | g17096.t3.CDS1 | 12452070 | 12453134 |
| chr_4 | g17096 | g17096.t3 | exon | g17096.t3.exon2 | 12453391 | 12453753 |
| chr_4 | g17096 | g17096.t3 | cds | g17096.t3.CDS2 | 12453391 | 12453753 |
| chr_4 | g17096 | g17096.t3 | exon | g17096.t3.exon3 | 12453830 | 12453906 |
| chr_4 | g17096 | g17096.t3 | cds | g17096.t3.CDS3 | 12453830 | 12453871 |
| chr_4 | g17096 | g17096.t3 | TTS | g17096.t3 | 12453989 | 12453989 |
Sequences
>g17096.t3 Gene=g17096 Length=1505
ATGCAAAAACCAACTTTCAATAAAATCACAAAAATTTGGAGTGGTCCAAAAGTTCTACCA
ATTTTCAATCCTGATCAAAATCTTGGTCAATTAATTCTAAAAGTTCTCGAGCAAACTTCT
GAAACTGTGGCACAAATTTCAGCTGATACAAAAGTTTCAGTCACTTGCGGTCAAATGCGA
GAAAGAACTGAAAAATTCGCGAAATATTTGAACAGTCTTGGACTCAAGCAAGACGATGTT
GTTGGAATTGTTGCTGCAAATACTGAAAATCTTGCTCCATCTGTTTTTGCTTGTTTTCTA
CTTGGACTGCCTTTTAATCCATTGGCACCAATCATGATTGAAAGTGACATTGTGCATATG
TTTGGCAAAACTAAACCAAAATTAATCATTTGTGATGGCAATAATTTAAAAATTGTTCAA
AATGGTGTGAATATGATGAAAAGTAATGCAAAAATTATTACAGTGATGGAAGATGTTGAA
AATTATGATTCAGTGACAAAAATATTGAACAGAGCAGCAGAGAAAGATTTTGATTATCCT
GAAGTCGACTCTAATTCAGCTGCATTAATTTTATGTTCATCTGGATCAATTTCAGTACCT
AAAGTAATCTTCAAAACTCACAAAGAAATTTTATCAATAAGATTTCCAATTTCGCAGAAT
CAAATTTGTTATGTATTGGCGTCAATTTTTTGGTACAGCGGATTTTCTAATTTGATTAAT
TCTGTTTTATTTAAACTAACAAGAGTTATCACTGCACAACCTTATAATCCACAGTATTTT
GTGGATATTTTAAGCACTTATGGAGTAAATATGACACTTACTCCACCATTTATACTTGTT
AATTTATATCATAGCGGATCATTAAAAAGATTAGATGAAATCAAAACTTGGATTGTTTCA
GGTGCAAAAGTTTCAGAGGAAATTGTTGAAAAATGTTTGCCGTTTATTCCAAATGGTATA
TTTCTCAATTGTTATGGAAGTTCAGAAGCAAACTTAATTTCTATAAATAATCAAAAGAGA
AAATATGAGAGTTCCGGATTTCTTGTTCAAAACATTGATATTAAGATTGTCGATGAAAAT
GGAAATTCACTTGATTACAATCAACAAGGTGAAATTTGTATTAAAAGGTCTGTTCCATTT
CTTGGTTATTTAGATGAACCAGAGAAAACAAAAGAAGCTTATGATGGTGAATGGTTTAAG
ACTGGCGACATTGGTTACTTTGATGATGAAGACTTTTTTTATATTATTGACCGCAAAAAA
GAGATTTTAATATATCAAGGTTTTCTTACTACACCATCAGAATTAGAAGCAATAATAAAT
GAAATTGATGGAGTTATGAGCAGTTGTGTTGTTGGAGTTCATCAAGAAAGTATTGCAAGT
GACATCATTTATGTTTTTGTAATTGTTGATAAAACTAAAAATTTAACAAAAATTTTCCAC
TTACCGCATCTGAAAAAGTTAATAGAATGAAAATTAAGGAAATGGCTAAAGAGTTAATGG
CTTAA
>g17096.t3 Gene=g17096 Length=489
MQKPTFNKITKIWSGPKVLPIFNPDQNLGQLILKVLEQTSETVAQISADTKVSVTCGQMR
ERTEKFAKYLNSLGLKQDDVVGIVAANTENLAPSVFACFLLGLPFNPLAPIMIESDIVHM
FGKTKPKLIICDGNNLKIVQNGVNMMKSNAKIITVMEDVENYDSVTKILNRAAEKDFDYP
EVDSNSAALILCSSGSISVPKVIFKTHKEILSIRFPISQNQICYVLASIFWYSGFSNLIN
SVLFKLTRVITAQPYNPQYFVDILSTYGVNMTLTPPFILVNLYHSGSLKRLDEIKTWIVS
GAKVSEEIVEKCLPFIPNGIFLNCYGSSEANLISINNQKRKYESSGFLVQNIDIKIVDEN
GNSLDYNQQGEICIKRSVPFLGYLDEPEKTKEAYDGEWFKTGDIGYFDDEDFFYIIDRKK
EILIYQGFLTTPSELEAIINEIDGVMSSCVVGVHQESIASDIIYVFVIVDKTKNLTKIFH
LPHLKKLIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g17096.t3 | Gene3D | G3DSA:3.40.50.12780 | - | 10 | 422 | 1.5E-83 |
| 2 | g17096.t3 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 4 | 474 | 2.2E-110 |
| 3 | g17096.t3 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 4 | 474 | 2.2E-110 |
| 1 | g17096.t3 | Pfam | PF00501 | AMP-binding enzyme | 37 | 425 | 3.7E-65 |
| 5 | g17096.t3 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 190 | 201 | - |
| 4 | g17096.t3 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 14 | 473 | 7.2E-87 |
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. There were no conditions that were differentially expressed