General information for g17096.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable 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.t4 | TSS | g17096.t4 | 12452030 | 12452030 |
| chr_4 | g17096 | g17096.t4 | isoform | g17096.t4 | 12452070 | 12453906 |
| chr_4 | g17096 | g17096.t4 | exon | g17096.t4.exon1 | 12452070 | 12452501 |
| chr_4 | g17096 | g17096.t4 | exon | g17096.t4.exon2 | 12452590 | 12453134 |
| chr_4 | g17096 | g17096.t4 | cds | g17096.t4.CDS1 | 12452880 | 12453134 |
| chr_4 | g17096 | g17096.t4 | exon | g17096.t4.exon3 | 12453391 | 12453906 |
| chr_4 | g17096 | g17096.t4 | cds | g17096.t4.CDS2 | 12453391 | 12453906 |
| chr_4 | g17096 | g17096.t4 | TTS | g17096.t4 | 12453989 | 12453989 |
Sequences
>g17096.t4 Gene=g17096 Length=1493
ATGCAAAAACCAACTTTCAATAAAATCACAAAAATTTGGAGTGGTCCAAAAGTTCTACCA
ATTTTCAATCCTGATCAAAATCTTGGTCAATTAATTCTAAAAGTTCTCGAGCAAACTTCT
GAAACTGTGGCACAAATTTCAGCTGATACAAAAGTTTCAGTCACTTGCGGTCAAATGCGA
GAAAGAACTGAAAAATTCGCGAAATATTTGAACAGTCTTGGACTCAAGCAAGACGATGTT
GTTGGAATTGTTGCTGCAAATACTGAAAATCTTGCTCCATCTGTTTTTGCTTGTTTTCTA
CTTGGACTGCCTTTTAATCCATTGGCACCAATCATGATTGAAAGTGACATTGTGCATATG
TTTGGCAAAACTAAACCAAAATTAATCATTTGTGATGGCAATAATTTAAAAATTGTTCAA
AATGGTGTGAATAGAAAGATTTTGATTATCCTGAAGTCGACTCTAATTCAGCTGCATTAA
TTTTATGTTCATCTGGATCAATTTCAGTACCTAAAGTAATCTTCAAAACTCACAAAGAAA
TTTTATCAATAAGATTTCCAATTTCGCAGAATCAAATTTGTTATGTATTGGCGTCAATTT
TTTGGTACAGCGGATTTTCTAATTTGATTAATTCTGTTTTATTTAAACTAACAAGAGTTA
TCACTGCACAACCTTATAATCCACAGTATTTTGTGGATATTTTAAGCACTTATGGAGTAA
ATATGACACTTACTCCACCATTTATACTTGTTAATTTATATCATAGCGGATCATTAAAAA
GATTAGATGAAATCAAAACTTGGATTGTTTCAGGTGCAAAAGTTTCAGAGGAAATTGTTG
AAAAATGTTTGCCGTTTATTCCAAATGGTATATTTCTCAATTGTTATGGAAGTTCAGAAG
CAAACTTAATTTCTATAAATAATCAAAAGAGAAAATATGAGAGTTCCGGATTTCTTGTTC
AAAACATTGATATTAAGATTGTCGATGAAAATGGAAATTCACTTGATTACAATCAACAAG
GTGAAATTTGTATTAAAAGGTCTGTTCCATTTCTTGGTTATTTAGATGAACCAGAGAAAA
CAAAAGAAGCTTATGATGGTGAATGGTTTAAGACTGGCGACATTGGTTACTTTGATGATG
AAGACTTTTTTTATATTATTGACCGCAAAAAAGAGATTTTAATATATCAAGGTTTTCTTA
CTACACCATCAGAATTAGAAGCAATAATAAATGAAATTGATGGAGTTATGAGCAGTTGTG
TTGTTGGAGTTCATCAAGAAAGTATTGCAAGTGACATCATTTATGTTTTTGTAATTGTTG
ATAAAACTAAAAATTTAACAGTAGCTCAAATTGAAAATTTTTTCAATTTAAAAGTCAAGA
AACAAAGACAACTTCAAGGTGGTGTTCATTTTCTAGAAAATTTTCCACTTACCGCATCTG
AAAAAGTTAATAGAATGAAAATTAAGGAAATGGCTAAAGAGTTAATGGCTTAA
>g17096.t4 Gene=g17096 Length=256
MTLTPPFILVNLYHSGSLKRLDEIKTWIVSGAKVSEEIVEKCLPFIPNGIFLNCYGSSEA
NLISINNQKRKYESSGFLVQNIDIKIVDENGNSLDYNQQGEICIKRSVPFLGYLDEPEKT
KEAYDGEWFKTGDIGYFDDEDFFYIIDRKKEILIYQGFLTTPSELEAIINEIDGVMSSCV
VGVHQESIASDIIYVFVIVDKTKNLTVAQIENFFNLKVKKQRQLQGGVHFLENFPLTASE
KVNRMKIKEMAKELMA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g17096.t4 | Gene3D | G3DSA:3.40.50.12780 | - | 1 | 151 | 0 |
| 6 | g17096.t4 | Gene3D | G3DSA:3.30.300.30 | - | 152 | 255 | 0 |
| 2 | g17096.t4 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 4 | 253 | 0 |
| 3 | g17096.t4 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 4 | 253 | 0 |
| 1 | g17096.t4 | Pfam | PF00501 | AMP-binding enzyme | 3 | 155 | 0 |
| 4 | g17096.t4 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 3 | 254 | 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. There were no conditions that were differentially expressed