General information for g11786.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable 4-coumarate–CoA ligase 3.
Parent gene
- The parent gene g11786 is located on chr_1: 18413562..18419558 (- 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 | g11786 | g11786.t4 | isoform | g11786.t4 | 18409806 | 18415374 |
| chr_1 | g11786 | g11786.t4 | exon | g11786.t4.exon1 | 18409806 | 18410472 |
| chr_1 | g11786 | g11786.t4 | exon | g11786.t4.exon2 | 18413382 | 18415374 |
| chr_1 | g11786 | g11786.t4 | cds | g11786.t4.CDS1 | 18413562 | 18414500 |
| chr_1 | g11786 | g11786.t4 | TSS | g11786.t4 | 18415404 | 18415404 |
| chr_1 | g11786 | g11786.t4 | TTS | g11786.t4 | NA | NA |
Sequences
>g11786.t4 Gene=g11786 Length=2660
ATGGTTCATTATGATCCAATAACAAGAATTTTACATGGCCCAAAACTGCCACAGGTCTAT
AGCTCAAATGTAACACTTGGTCAAGTGATATTAAAAAAACTTTATAAAACACCTGACAAG
GTGATACAAGTGTGTGATGATGATGGAATAGAATTAACGTGCTCTCAAATGACAAAATAC
ATGATAAATATAGCTAAAAACCTTTCAAAACTTGGTTTTCAAAGTGGTGATATTGCTGGT
CTTCTAGCTGTTTGGAGCACTTATACAGCTCCTACTATTTTTGCTTGCTCCCTACTTTCT
ATGCCATTAAATCCAATAGATACATCGTTTAGTGTGAATCAAATTGTTCATATTTATAGA
CAAACACAACCAAAAATTGTATTTTGTGATCACGATGTGATTGATAAATTAATGGCAGCA
TTAGGCATTCTTGAGAGCGAAGCAACAATTGTTATTTTAACGGAGCGTATCAATGGATTA
TTACATGTCAGTGATTTACTACACGATTGTGATGTGAGTGATGAGTAAGTATCTTAATTT
ATGTGTTGATCAATAATTTCTTATCTAATATTGTTGATTAAATATATTCAATATAATACG
TAAATTTTCATCTATCATAAATTTAATCGATTTAAAATACATTTTTTCCTCATGAATTAA
AATTCCACACCTGTAACAACAAACAGTTTTAAATTTATTTTATTCTTGTTATTTTAGCTT
TATTTATCAAACACACTCGAATGAGAAGTGCTCTCTTATCATTTGCACATCGGGAAGTTC
GGGAAATCCAAAACTAGCATGTTTAACACATTTACAACAACTTCAAAATTTTACATGGAT
TAATAACTTCAACCCAGATTTTTTTTCATTCAATATGACAAGTCCATATTGGTTAAGTGG
ACTTAATTGTATGATATTTCAGTTTTTACATGGTCGTAAAAGACTGATAACTTCAAAACC
ATATACTCCAGAAACTTTTTTGAATTTGATTGAAAAGTATAAAATCAACGATACTTTTTT
AGTTCCTCCACTTTTGTCTTTACTTATTGATACACCAAGATTTAAAGAAGCCGATCTTAG
TTCAATTAAATATTTTGTAACTGGAGGCCTTTATGTATCAGAAAATTTAAGGATCGTAGT
TCAACAAAAACTAATAAATGGAAAAATTAAAATTGGATATGGTATGACAGAATTTGGAGG
ACTTCTTGCTGAAACGCAAGATGAATTTCATTTAGGAACATCAGTTGGATATCCAACACA
CAATACTGAAGTGAAAATTCAACTTGATGATGGAACTTCTGGTGGTATATCAGAAATTGG
AGAAATTTTAGTACGCCATCCAGTTCGATTTCTTGGTTACTATAAAAATTGTCATAAAAA
CATTATTGATGACGAAGGTTGGTTGCATACAAGTGACATGGGATTTATTGATAAATATCA
TGAAATAAATATTATTGGTCAGCGAATATTTGCTATAAAAAGTTTCTATAATGAATTCTT
TCCAAGTGAAGTAGAAGAAATTATTGAAGCAGTTGATGGTGTAAAGCAAGTTGTAATTGT
CGGAACACCGGATCCAGTTGATATTGAAAAAACTACAGCTCTTATAGTGAAAGAACCAAA
TAGTAATGTTACAGAAGACTTAATATATGAAGCGACAAGCACTCTACCTATTTATAAACA
GCCTCGAGGAGGAATATTTTTTCTAGACAATCTACCACTTACTTCGACTGGAAAAATCAA
ACGAAAAGAGGCAAAGGAGCTTGCTAAAAAGCTCACTTTTGAAAGAAATAATCATAATGA
TTTACCTGCTTAGCTCGTCTGTTTCTTCATCATTGCTCCTATACACCTCTGTCGAGTTTA
CGACTGTTTCAAATGTCGACAATGTTGTACTTAAAATGTCATTTGGATAATGATTCTCCC
CATATTGTGCTCGAAATCCACTGTTATCTATACCAAAACGATTCATTTTTGCTTCAATAA
GGTTCATATAACTTCTTAAGATGTATTTCTTTTTTGCAAATAAGTTGTTCTTTCTGAATA
TTATTGTTTCAAAATGTACATTGATTTTTTAACTAACTAAATATTGCTTTGACAATTTGA
AGAATAATAAAGTAAAAAATGCACAAAAGAATTAACTTCACTTTGTTATCCATAATTTTC
GACTTAATATTGCTTAATAAATATTAAAATTTCAAAATGTCTTTAGCATTTTTTTAAATT
CACTCTATTTCTATTTGTTACACAAATTTCAATGATAATTGATAATTGTTCAATTATACA
TTATCACACAACGACATAGAACATTTATAATCTTTTTAACCGCCGAAAAAATGATTAAGA
CATATGAACAGTCCTACTCTCAAATAAAAACTGAACACAAAAAATGCTTTAAACAACAAA
CTCCGGTGTGCATGCAACACGATGGTAGTAAAAAATTAAAGAAATGAGATATAAACAGTA
GAGAAAAAGAGAGAGAGAAATATGAGAAATGTAAGCAACAAACATTTTTTTCTATAGTAA
AATGATTTAACTACAATACATGAGAGCATTTGACAAAAATATGTATGTATGGCTGTATAA
GTCATAATTGTGAGAGAAATAAAAAGAGAGACACTCATGCGACAGTGACTTTAAAATAAA
GCTATTTAGTAAATGACTCA
>g11786.t4 Gene=g11786 Length=312
MTSPYWLSGLNCMIFQFLHGRKRLITSKPYTPETFLNLIEKYKINDTFLVPPLLSLLIDT
PRFKEADLSSIKYFVTGGLYVSENLRIVVQQKLINGKIKIGYGMTEFGGLLAETQDEFHL
GTSVGYPTHNTEVKIQLDDGTSGGISEIGEILVRHPVRFLGYYKNCHKNIIDDEGWLHTS
DMGFIDKYHEINIIGQRIFAIKSFYNEFFPSEVEEIIEAVDGVKQVVIVGTPDPVDIEKT
TALIVKEPNSNVTEDLIYEATSTLPIYKQPRGGIFFLDNLPLTSTGKIKRKEAKELAKKL
TFERNNHNDLPA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11786.t4 | Gene3D | G3DSA:3.40.50.12780 | - | 1 | 194 | 0 |
| 7 | g11786.t4 | Gene3D | G3DSA:3.30.300.30 | - | 195 | 302 | 0 |
| 3 | g11786.t4 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 2 | 299 | 0 |
| 4 | g11786.t4 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 2 | 299 | 0 |
| 2 | g11786.t4 | Pfam | PF00501 | AMP-binding enzyme | 3 | 197 | 0 |
| 1 | g11786.t4 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 212 | 287 | 0 |
| 5 | g11786.t4 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 2 | 300 | 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.
