General information for g10240.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 1-2-dihydroxy-3-keto-5-methylthiopentene dioxygenase.
Parent gene
- The parent gene g10240 is located on chr_1: 8456092..8458159 (- 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 | g10240 | g10240.t13 | TTS | g10240.t13 | 8455849 | 8455849 |
| chr_1 | g10240 | g10240.t13 | isoform | g10240.t13 | 8455864 | 8458159 |
| chr_1 | g10240 | g10240.t13 | exon | g10240.t13.exon1 | 8455864 | 8456001 |
| chr_1 | g10240 | g10240.t13 | cds | g10240.t13.CDS1 | 8455864 | 8456001 |
| chr_1 | g10240 | g10240.t13 | exon | g10240.t13.exon2 | 8456080 | 8456173 |
| chr_1 | g10240 | g10240.t13 | cds | g10240.t13.CDS2 | 8456080 | 8456173 |
| chr_1 | g10240 | g10240.t13 | exon | g10240.t13.exon3 | 8456556 | 8456683 |
| chr_1 | g10240 | g10240.t13 | cds | g10240.t13.CDS3 | 8456556 | 8456683 |
| chr_1 | g10240 | g10240.t13 | exon | g10240.t13.exon4 | 8456829 | 8456906 |
| chr_1 | g10240 | g10240.t13 | cds | g10240.t13.CDS4 | 8456829 | 8456885 |
| chr_1 | g10240 | g10240.t13 | exon | g10240.t13.exon5 | 8457964 | 8457999 |
| chr_1 | g10240 | g10240.t13 | exon | g10240.t13.exon6 | 8458051 | 8458159 |
| chr_1 | g10240 | g10240.t13 | TSS | g10240.t13 | 8458256 | 8458256 |
Sequences
>g10240.t13 Gene=g10240 Length=583
ATGGTGAGAGCATGGTTCATGGATAATGATGTTGAATCAGATCAACGATTAGAGCATCAC
CGTTCACCACCTGAATTTGTCGATTTAGACAAATTATTCGAGCTTACTGACTGAGAGCAT
TAAATGTTTTTTTCTTCCTATTATTTTTGATCCTGAGAGTGTTGAAATGCAAAATAAATT
AAATGAATTGAGAAAATCAAGAGGATATTCATTTGAGGATGAGATAACATGCTCGAAGGA
GTGCCTACCTGACTATGAGAACAAATTGAAAAGTTTTTACGAAGAACATTTGCATACTGA
TGAAGAAATTCGTTATGTCTTAGAGGGTCAGGGATATTTCGATGTACGAGACGGTCAGGA
TCGGTGGATACGTATAGAAGTGATCAAGGGTGACTTGATTATAATTCCAGCTGGAATTTA
TCATCGCTTTACACTTAATGTTAATAACTTCATCAAAGCAAAAAGATATTTTGTTGGAGA
GCCTGTTTGGAAGCCATACAACCGAGAGCCATCGACTGATTTTATGGAATGCAGAGTTAA
TTATAAAAAGCAACTCGATAATGGATTCGAAATAAAAAGCTGA
>g10240.t13 Gene=g10240 Length=138
MQNKLNELRKSRGYSFEDEITCSKECLPDYENKLKSFYEEHLHTDEEIRYVLEGQGYFDV
RDGQDRWIRIEVIKGDLIIIPAGIYHRFTLNVNNFIKAKRYFVGEPVWKPYNREPSTDFM
ECRVNYKKQLDNGFEIKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10240.t13 | CDD | cd02232 | cupin_ARD | 1 | 110 | 0.00000 |
| 6 | g10240.t13 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 1 | 133 | 0.00000 |
| 4 | g10240.t13 | Hamap | MF_03154 | 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase [ADI1]. | 1 | 120 | 25.78349 |
| 2 | g10240.t13 | PANTHER | PTHR23418:SF0 | 1,2-DIHYDROXY-3-KETO-5-METHYLTHIOPENTENE DIOXYGENASE | 3 | 130 | 0.00000 |
| 3 | g10240.t13 | PANTHER | PTHR23418 | ACIREDUCTONE DIOXYGENASE | 3 | 130 | 0.00000 |
| 1 | g10240.t13 | Pfam | PF03079 | ARD/ARD’ family | 2 | 109 | 0.00000 |
| 5 | g10240.t13 | SUPERFAMILY | SSF51182 | RmlC-like cupins | 4 | 132 | 0.00000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0010309 | acireductone dioxygenase [iron(II)-requiring] activity | MF |
| GO:0019509 | L-methionine salvage from methylthioadenosine | BP |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K08967 (1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase)
Pathway
- This transcript belongs to the following pathways
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.
