Gene loci information

Transcript annotation

  • This transcript has been annotated as 1_2-dihydroxy-3-keto-5-methylthiopentene dioxygenase.

Parent gene

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.t9 TTS g10240.t9 8455849 8455849
chr_1 g10240 g10240.t9 isoform g10240.t9 8455864 8458159
chr_1 g10240 g10240.t9 exon g10240.t9.exon1 8455864 8456001
chr_1 g10240 g10240.t9 cds g10240.t9.CDS1 8455864 8456001
chr_1 g10240 g10240.t9 exon g10240.t9.exon2 8456080 8456173
chr_1 g10240 g10240.t9 cds g10240.t9.CDS2 8456080 8456173
chr_1 g10240 g10240.t9 exon g10240.t9.exon3 8456556 8456683
chr_1 g10240 g10240.t9 cds g10240.t9.CDS3 8456556 8456683
chr_1 g10240 g10240.t9 exon g10240.t9.exon4 8456829 8456906
chr_1 g10240 g10240.t9 cds g10240.t9.CDS4 8456829 8456906
chr_1 g10240 g10240.t9 exon g10240.t9.exon5 8458049 8458159
chr_1 g10240 g10240.t9 cds g10240.t9.CDS5 8458049 8458159
chr_1 g10240 g10240.t9 TSS g10240.t9 8458256 8458256

Sequences

>g10240.t9 Gene=g10240 Length=549
ATGGTGAGAGCATGGTTCATGGATAATGATGTTGAATCAGATCAACGATTAGAGCATCAC
CGTTCACCACCTGAATTTGTCGATTTAGACAAATTATTCGAGCTTACTGGTTTTGATCCT
GAGAGTGTTGAAATGCAAAATAAATTAAATGAATTGAGAAAATCAAGAGGATATTCATTT
GAGGATGAGATAACATGCTCGAAGGAGTGCCTACCTGACTATGAGAACAAATTGAAAAGT
TTTTACGAAGAACATTTGCATACTGATGAAGAAATTCGTTATGTCTTAGAGGGTCAGGGA
TATTTCGATGTACGAGACGGTCAGGATCGGTGGATACGTATAGAAGTGATCAAGGGTGAC
TTGATTATAATTCCAGCTGGAATTTATCATCGCTTTACACTTAATGTTAATAACTTCATC
AAAGCAAAAAGATATTTTGTTGGAGAGCCTGTTTGGAAGCCATACAACCGAGAGCCATCG
ACTGATTTTATGGAATGCAGAGTTAATTATAAAAAGCAACTCGATAATGGATTCGAAATA
AAAAGCTGA

>g10240.t9 Gene=g10240 Length=182
MVRAWFMDNDVESDQRLEHHRSPPEFVDLDKLFELTGFDPESVEMQNKLNELRKSRGYSF
EDEITCSKECLPDYENKLKSFYEEHLHTDEEIRYVLEGQGYFDVRDGQDRWIRIEVIKGD
LIIIPAGIYHRFTLNVNNFIKAKRYFVGEPVWKPYNREPSTDFMECRVNYKKQLDNGFEI
KS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10240.t9 CDD cd02232 cupin_ARD 33 154 0.00000
6 g10240.t9 Gene3D G3DSA:2.60.120.10 Jelly Rolls 1 177 0.00000
4 g10240.t9 Hamap MF_03154 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase [ADI1]. 2 164 35.00828
2 g10240.t9 PANTHER PTHR23418:SF0 1,2-DIHYDROXY-3-KETO-5-METHYLTHIOPENTENE DIOXYGENASE 1 174 0.00000
3 g10240.t9 PANTHER PTHR23418 ACIREDUCTONE DIOXYGENASE 1 174 0.00000
1 g10240.t9 Pfam PF03079 ARD/ARD’ family 3 153 0.00000
5 g10240.t9 SUPERFAMILY SSF51182 RmlC-like cupins 1 176 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

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. There were no conditions that were differentially expressed