General information for g12857.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable 4-coumarate–CoA ligase 1.
Parent gene
- The parent gene g12857 is located on chr_1: 26577322..26578391 (- 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 | g12857 | g12857.t2 | isoform | g12857.t2 | 26577322 | 26578391 |
| chr_1 | g12857 | g12857.t2 | exon | g12857.t2.exon1 | 26577322 | 26577959 |
| chr_1 | g12857 | g12857.t2 | cds | g12857.t2.CDS1 | 26577322 | 26577959 |
| chr_1 | g12857 | g12857.t2 | exon | g12857.t2.exon2 | 26578011 | 26578218 |
| chr_1 | g12857 | g12857.t2 | cds | g12857.t2.CDS2 | 26578011 | 26578218 |
| chr_1 | g12857 | g12857.t2 | exon | g12857.t2.exon3 | 26578275 | 26578391 |
| chr_1 | g12857 | g12857.t2 | cds | g12857.t2.CDS3 | 26578275 | 26578391 |
| chr_1 | g12857 | g12857.t2 | TSS | g12857.t2 | 26578429 | 26578429 |
| chr_1 | g12857 | g12857.t2 | TTS | g12857.t2 | NA | NA |
Sequences
>g12857.t2 Gene=g12857 Length=963
ATGAAAGTAAAAGATAACATTTTGTATGCCGGTGATTACGACAAAAAATTTAATTTCTAC
TCTTTGGGGCATTTTGTTATCAATTCGCTAAAACATGGAGGTGATCGTGAAGCACTTGTC
AACGGTGCAACCGGTTTGTCATGGACTTATGCAGACATTCTAGAAGAAACAAATAAATAT
GCAAGATCATTTTTTGCTTTCGGAATTAGAAGAAATGATAGAATTGCAATTATCTCAGAA
AATCGTCATGAAGTTGCAGCGATCACTTTTGCTGCTTTTTGTCTTAATGCTATTGTTTCT
CCAATCAATTATACTTATACAAAACGTGAATTGCAACATGCTTTGAAATTATCTCAACCT
AAAATTGTGATCGTATCAGAAACTTCAGCAAAAACTACTATCGATGTATGCAAGGAATTA
AAATTTGTAGAAAAAATAATTCTCCTTGATAAAATCACTGAGACTTACTCAAGTGACGAT
CGCGTAATTTCGGTCATTGACTTCAATCGTCAATATGAGTTGAATTCTTTCTTTCTAAAT
TACGTCATAGCAGAACAAACTGATGTTGATGAACAAACTGCAATGATTTTTTTATCAAGT
GGTACAACTGATCTATCTAAAGGATGTGAAACAACCGGAGGAAATTTATTCAAAGTTATT
GATCAATATTCTTCAAGTTTATTAAATCATAAAAGATTTGATGAAAGAATAACAACTTTA
AACATTGCGCCATGGTTCCATATTATGGGCTTCACAAATCTTTTTCTGATTCTTTCTTCC
AACAGATTTCGATGCATCTTTTTACCTAAATTTGATCTTAGTCTATTTTTAAGTTCTATT
CAAAAATATAAAGTATCTTCAATGACTATTCCACCACCTGTCGTTATTCTTCTTGCTAAA
AATCCACTAGTTGATAAATTTGACTTGTCAAGTTTGAAATTAATCTTATCTGGTGCTGCT
CCT
>g12857.t2 Gene=g12857 Length=321
MKVKDNILYAGDYDKKFNFYSLGHFVINSLKHGGDREALVNGATGLSWTYADILEETNKY
ARSFFAFGIRRNDRIAIISENRHEVAAITFAAFCLNAIVSPINYTYTKRELQHALKLSQP
KIVIVSETSAKTTIDVCKELKFVEKIILLDKITETYSSDDRVISVIDFNRQYELNSFFLN
YVIAEQTDVDEQTAMIFLSSGTTDLSKGCETTGGNLFKVIDQYSSSLLNHKRFDERITTL
NIAPWFHIMGFTNLFLILSSNRFRCIFLPKFDLSLFLSSIQKYKVSSMTIPPPVVILLAK
NPLVDKFDLSSLKLILSGAAP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12857.t2 | Gene3D | G3DSA:3.40.50.980 | - | 50 | 212 | 0 |
| 5 | g12857.t2 | Gene3D | G3DSA:3.40.50.980 | - | 219 | 321 | 0 |
| 2 | g12857.t2 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 21 | 321 | 0 |
| 3 | g12857.t2 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 21 | 321 | 0 |
| 1 | g12857.t2 | Pfam | PF00501 | AMP-binding enzyme | 32 | 321 | 0 |
| 4 | g12857.t2 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 19 | 321 | 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