General information for g12835.t29
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable methylthioribulose-1-phosphate dehydratase.
Parent gene
- The parent gene g12835 is located on chr_1: 26473115..26475008 (- 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 | g12835 | g12835.t29 | TTS | g12835.t29 | 26473084 | 26473084 |
| chr_1 | g12835 | g12835.t29 | isoform | g12835.t29 | 26473115 | 26473673 |
| chr_1 | g12835 | g12835.t29 | exon | g12835.t29.exon1 | 26473115 | 26473432 |
| chr_1 | g12835 | g12835.t29 | cds | g12835.t29.CDS1 | 26473115 | 26473432 |
| chr_1 | g12835 | g12835.t29 | exon | g12835.t29.exon2 | 26473499 | 26473673 |
| chr_1 | g12835 | g12835.t29 | cds | g12835.t29.CDS2 | 26473499 | 26473618 |
| chr_1 | g12835 | g12835.t29 | TSS | g12835.t29 | 26474672 | 26474672 |
Sequences
>g12835.t29 Gene=g12835 Length=493
GGTCACACCACCTGATTATAAAAAATTGAAAAAATCTCAATGTACACCACTCTTCATGAT
CGCGTATAAAATGCGAAATGCAGGCTCTGTAATTCATACTCACTCACCTAATGCAGTTAT
GGCTACATTGCTTTATGAAAAAGAATTTAAAATAACTCATCAAGAAATGATTAAGGGAAT
TTTCGATTACGAATTAAATCGTTATTTGAGATATGATGAGGAACTTGTAGTTCCGATCAT
TGAAAATACAAATCAAGAGAGAGACTTGGAAGAGAGCTCATATAACGCAATAAAGGAATA
TCCAGGAACGTCTGCCGTTCTAGTAAGACGTCATGGCATTTATGTTTGGGGAAAATCATG
GCAATCAGCAAAAACACAATGTGAATGTTATGACTATTTATTCAATATTGCTCTTGAAAT
GAAAAAATTTGGTCTAGATCCAAGCGCCATACCATCATCTAATTCTTCTCAAACAAAAAC
CAACAAAAAATAA
>g12835.t29 Gene=g12835 Length=145
MIAYKMRNAGSVIHTHSPNAVMATLLYEKEFKITHQEMIKGIFDYELNRYLRYDEELVVP
IIENTNQERDLEESSYNAIKEYPGTSAVLVRRHGIYVWGKSWQSAKTQCECYDYLFNIAL
EMKKFGLDPSAIPSSNSSQTKTNKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g12835.t29 | Gene3D | G3DSA:3.40.225.10 | - | 1 | 140 | 0 |
| 2 | g12835.t29 | PANTHER | PTHR10640 | METHYLTHIORIBULOSE-1-PHOSPHATE DEHYDRATASE | 1 | 138 | 0 |
| 1 | g12835.t29 | Pfam | PF00596 | Class II Aldolase and Adducin N-terminal domain | 3 | 120 | 0 |
| 3 | g12835.t29 | SUPERFAMILY | SSF53639 | AraD/HMP-PK domain-like | 3 | 134 | 0 |
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:0046872 | metal ion binding | MF |
| GO:0019509 | L-methionine salvage from methylthioadenosine | BP |
| GO:0005737 | cytoplasm | CC |
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.
