General information for g17097.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 4-coumarate–CoA ligase 1.
Parent gene
- The parent gene g17097 is located on chr_4: 12454885..12456704 (+ 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 | g17097 | g17097.t1 | TSS | g17097.t1 | 12454829 | 12454829 |
| chr_4 | g17097 | g17097.t1 | isoform | g17097.t1 | 12454885 | 12456704 |
| chr_4 | g17097 | g17097.t1 | exon | g17097.t1.exon1 | 12454885 | 12455961 |
| chr_4 | g17097 | g17097.t1 | cds | g17097.t1.CDS1 | 12454885 | 12455961 |
| chr_4 | g17097 | g17097.t1 | exon | g17097.t1.exon2 | 12456192 | 12456704 |
| chr_4 | g17097 | g17097.t1 | cds | g17097.t1.CDS2 | 12456192 | 12456704 |
| chr_4 | g17097 | g17097.t1 | TTS | g17097.t1 | 12456895 | 12456895 |
Sequences
>g17097.t1 Gene=g17097 Length=1590
ATGCAAAAACCAACTTTTGATAAAATCACAAAAGTTTGGAGTGGTCCAAAAGTTCCACCA
TTTTTCAATCCTGATCAAAATCTTGGTCAATTAATTCTAAAAGTTCTCGAGCAAACTCCT
GAAACTGTGACACAAATTTCAGCTGATACAAAAGTTTCAGTCACTTGCGGTCAAATGCGA
GAAAGAACTGAAAAATTCGCGAAATATTTAAACAGTCTTGGACTCAAGCAAGGCGATGTT
GTTGGAATTGTTGCTGCAAATACTGAAAATCTTGCTCCAGCTGTTTTTGCTTGCTTTTTA
CTTGGACTTCCTGTTAATCCATTGGCACCTATGATGATTGAAAGTGACATTGTCCATATG
TTTGGTAAAACTAAACCAAAATTGATTCTTTGTGATGAAAACTGTTTAAAAATTGTTCAA
AATGCTGTGAATATGATGAAAAGTGATGCAAAAATTATTACAGTGATGGAAGATGTTGAA
AATTATGATTCAGTGACAAAAATATTAAACAGAGCAGCAGAGAAAGACTTTGAATATCCT
GAAATTGATTCAAATTCAATTTTAGTAATTTTATGCTCATCTGGATCAACAGGTTTACCA
AAAGGAGTTTGGAAGACACACAAAGAATTCATCATTGCTTCTGACACTCGTAATTTTAAT
GGAATGGAAAATTCAGTCATTTTTCAAGCTTCACAAATTTTTTGGATCAGTGGAATCTTT
CTTTTAATTTTTTGTGCTTTGTATAAACAAACAAGAATTATAACTTCTCAACCTTGTGAT
CCACACAATTTTATTAATATTTTGAAAACTTACAAAGTAAATGTGACCAGCACTCCACCA
TATCTTCTTGTCAATTTACTTCAAAGCAAAGCATTTGAAAAATTAGATGAAATCAAAACT
TGGTCCATTTTAGGTGCAAAAGTTTCAAAAGAAATTGTTGAAAAATTTTTGCCTTTTATT
CCAAATGGTATTTTTGTTAATGGTTATGGATGTACCGAAGCAAATTCAATTTCTGCAAAT
TGTCAGATGAGAAAGTATGAAAGTTGTGGATTTCCTTCTAAAAATGTTGAAATTAAGATT
GTTGATGAAAATGGAAATTCACTTGATAGAAATCAGCAAGGTGAAATTTATGTCAAATGG
TCTGTTCCATTTCTTGGATATCTTCATGAACCTGAAAAAACTAAAGAAGTTTATGATGGT
GAATGGTTTAAGACAGGCGACATTGGTTACTTTGATGATGAAGACTTTCTTTATATTATT
GACCGTAAAAAAGAGATAATAAAAAATCAAGGAATCATCACTGCACCATCAGAGCTTGAA
GCAATCATAAATGAAATCGATGGAGTTATGAGCAGTTGTGTTGTTGGAATTTTAGAAGAA
TATTCTGGAGATGATATCATTCATGCTTTTGTAATTGTTGAAGAATCAAGTGGATTAACT
GAAAATTTTATTTTAAATTATGTCAATTCAAAAGTCATTGAGCAAAAGAAACTTCGCGGT
GGTGTTCATTTTATTGAAAAGTTTCCACTTACTGCATCTAAAAAAATTCATAGAATGAAA
ATTAAAGAAATGGCTAAAAATTTCCAATAA
>g17097.t1 Gene=g17097 Length=529
MQKPTFDKITKVWSGPKVPPFFNPDQNLGQLILKVLEQTPETVTQISADTKVSVTCGQMR
ERTEKFAKYLNSLGLKQGDVVGIVAANTENLAPAVFACFLLGLPVNPLAPMMIESDIVHM
FGKTKPKLILCDENCLKIVQNAVNMMKSDAKIITVMEDVENYDSVTKILNRAAEKDFEYP
EIDSNSILVILCSSGSTGLPKGVWKTHKEFIIASDTRNFNGMENSVIFQASQIFWISGIF
LLIFCALYKQTRIITSQPCDPHNFINILKTYKVNVTSTPPYLLVNLLQSKAFEKLDEIKT
WSILGAKVSKEIVEKFLPFIPNGIFVNGYGCTEANSISANCQMRKYESCGFPSKNVEIKI
VDENGNSLDRNQQGEIYVKWSVPFLGYLHEPEKTKEVYDGEWFKTGDIGYFDDEDFLYII
DRKKEIIKNQGIITAPSELEAIINEIDGVMSSCVVGILEEYSGDDIIHAFVIVEESSGLT
ENFILNYVNSKVIEQKKLRGGVHFIEKFPLTASKKIHRMKIKEMAKNFQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g17097.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 11 | 425 | 1.9E-96 |
| 9 | g17097.t1 | Gene3D | G3DSA:3.30.300.30 | - | 426 | 528 | 1.4E-15 |
| 3 | g17097.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 4 | 526 | 5.7E-134 |
| 4 | g17097.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 4 | 526 | 5.7E-134 |
| 2 | g17097.t1 | Pfam | PF00501 | AMP-binding enzyme | 36 | 429 | 4.7E-80 |
| 1 | g17097.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 438 | 515 | 4.1E-6 |
| 11 | g17097.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 225 | - |
| 12 | g17097.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 226 | 248 | - |
| 10 | g17097.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 249 | 529 | - |
| 7 | g17097.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 190 | 201 | - |
| 6 | g17097.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 11 | 527 | 9.81E-108 |
| 5 | g17097.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 226 | 248 | - |
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