General information for g1087.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 g1087 is located on chr_3: 8067536..8069181 (+ 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_3 | g1087 | g1087.t1 | isoform | g1087.t1 | 8067536 | 8069181 |
| chr_3 | g1087 | g1087.t1 | exon | g1087.t1.exon1 | 8067536 | 8068606 |
| chr_3 | g1087 | g1087.t1 | cds | g1087.t1.CDS1 | 8067536 | 8068606 |
| chr_3 | g1087 | g1087.t1 | exon | g1087.t1.exon2 | 8068663 | 8069181 |
| chr_3 | g1087 | g1087.t1 | cds | g1087.t1.CDS2 | 8068663 | 8069181 |
| chr_3 | g1087 | g1087.t1 | TSS | g1087.t1 | NA | NA |
| chr_3 | g1087 | g1087.t1 | TTS | g1087.t1 | NA | NA |
Sequences
>g1087.t1 Gene=g1087 Length=1590
ATGAACAAAACTACTTTCAATCAAGTAACAAAAGTCTGGAGCGGTCCAAAAGTACCACCA
ATCTTCAATCCAGATCAAAATCTTGGCCAATTGATTGTGAAAGTTCTTGAGCAAACTCCA
GATGCTGTGACACAAATTTCAGCTGATACAAATGTTTCAGTAACTTGTGGTGAAACGCGA
GAAAGAATTTTGAAATTCGCAGTTCATTTGAATAATTTGGGACTTAAACAAGGCGATGTT
ATTGGTGTTGTAGCTGGAAATACTGAAAATATTGCTCCAGCTGTTTTTGCTTGTTTTCTA
CTTGGACTTCCTGTTAATCCTTTAGCACCGGTCATGATTGAAAGTGACATTATGCAAATG
TATTTGAAAACTAAACCAAAATTGATCTTTTGTGATGAGAAAAATTTAAGAACTGTTCAA
AATTCAGTAGACATGATGAAAAGTGAAGCAAAAATTTATACAGTGATGGAAAAAGTTGAT
GGTTATGAATGTGTAACTGAAATACTCAAGAACGATATTAAGTTTGAAGATCTTATTTAT
CCAGAAGTTGATCCAAATTCAATTGTTTTTATTTCTTATACATCTGGTTCAACAGGATTT
CCTAAAGGAGTTGGTAGAACTCACAAGCAAATAATTTCTTATTTCATTCCTGTAACAAAT
GGTCCAAACATTTTGTATCAATCAATAGAAATTTTTTGGTTTTTTGGAATTTATTTTCTT
ATTCTTGGAACACTTTATAAATACATAAGAATAATAGCAGCTCAACCACCAACAGCCAAA
CTCATAGTTAATATTATCGAGAAATTCAAGGTCACACAAGTTTCTACTGGACCTTATCTC
GTTAATAATTTATTACAACTTGATAATTTAGAACTACTTGAGACGATAAAAATGTGGATG
ATTCCAGGAGCAAAAGCAAGTCAGCTTATTTGTGATAGACTTAAAAATTTTGTGCCTAAT
GGTTTAGTAAATCCCTGTTATGGCTCAACTGAATGTGATTTTATTACCACAAATTATAAT
GGAAAAAAATTAGGAAGTTGTGGTCAAGTTTTTTATAACAACCAAATTAAAATAATCGAT
GACAATGGAAATGCTCTTAGTAATAATCAACAAGGTGAAATTTGTGTCAAAAAAGTTCTT
GAATTTACTGGTTATTTGAATGAAACTGAAAATACAAAAGAAGTTTATGATGGTGAATGG
TTTAAGACAGGCGATTTTGGATATTTTGATGATGAAGGTTATCTTTATATTGTCGATCGA
AAGAAAGAACTTTTAAAATATAATTATATGCAAGTAGCACCATCAGAACTTGAAGCAATA
ATAAATGAAATTGATGGAGTTGTCAGCAGTTGTGTTGTTGGAGTTTTAGACGAAAATACA
GGAAATGACATAATTCATGCTTTTGTGATTGTCGATGAATTTTGTAAAATAACAGAACAA
GAAATTGAAGATTATGTTAGAAAAAGAGTCATTGATCAAAAAAGAATTCGAGGTGGCGTT
CATTTTGTAGAAAAATTTCCTCTAACAGCATCAGGAAAAGTTTATAGAAAAGAACTCAAG
AATTTGGCAGCTGAAAAATTTACAAAATAA
>g1087.t1 Gene=g1087 Length=529
MNKTTFNQVTKVWSGPKVPPIFNPDQNLGQLIVKVLEQTPDAVTQISADTNVSVTCGETR
ERILKFAVHLNNLGLKQGDVIGVVAGNTENIAPAVFACFLLGLPVNPLAPVMIESDIMQM
YLKTKPKLIFCDEKNLRTVQNSVDMMKSEAKIYTVMEKVDGYECVTEILKNDIKFEDLIY
PEVDPNSIVFISYTSGSTGFPKGVGRTHKQIISYFIPVTNGPNILYQSIEIFWFFGIYFL
ILGTLYKYIRIIAAQPPTAKLIVNIIEKFKVTQVSTGPYLVNNLLQLDNLELLETIKMWM
IPGAKASQLICDRLKNFVPNGLVNPCYGSTECDFITTNYNGKKLGSCGQVFYNNQIKIID
DNGNALSNNQQGEICVKKVLEFTGYLNETENTKEVYDGEWFKTGDFGYFDDEGYLYIVDR
KKELLKYNYMQVAPSELEAIINEIDGVVSSCVVGVLDENTGNDIIHAFVIVDEFCKITEQ
EIEDYVRKRVIDQKRIRGGVHFVEKFPLTASGKVYRKELKNLAAEKFTK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1087.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 10 | 423 | 3.6E-85 |
| 10 | g1087.t1 | Gene3D | G3DSA:3.30.300.30 | - | 424 | 528 | 6.3E-21 |
| 3 | g1087.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 4 | 525 | 1.3E-132 |
| 4 | g1087.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 4 | 525 | 1.3E-132 |
| 2 | g1087.t1 | Pfam | PF00501 | AMP-binding enzyme | 36 | 427 | 3.1E-72 |
| 1 | g1087.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 436 | 513 | 2.2E-12 |
| 12 | g1087.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 230 | - |
| 13 | g1087.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 249 | - |
| 11 | g1087.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 250 | 529 | - |
| 8 | g1087.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 191 | 202 | - |
| 7 | g1087.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 24 | 526 | 3.01E-101 |
| 6 | g1087.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 91 | 113 | - |
| 5 | g1087.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 224 | 246 | - |
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