General information for g12835.t1
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.t1 | TTS | g12835.t1 | 26473084 | 26473084 |
| chr_1 | g12835 | g12835.t1 | isoform | g12835.t1 | 26473115 | 26474493 |
| chr_1 | g12835 | g12835.t1 | exon | g12835.t1.exon1 | 26473115 | 26473432 |
| chr_1 | g12835 | g12835.t1 | cds | g12835.t1.CDS1 | 26473115 | 26473432 |
| chr_1 | g12835 | g12835.t1 | exon | g12835.t1.exon2 | 26473499 | 26473672 |
| chr_1 | g12835 | g12835.t1 | cds | g12835.t1.CDS2 | 26473499 | 26473672 |
| chr_1 | g12835 | g12835.t1 | exon | g12835.t1.exon3 | 26473729 | 26473850 |
| chr_1 | g12835 | g12835.t1 | cds | g12835.t1.CDS3 | 26473729 | 26473850 |
| chr_1 | g12835 | g12835.t1 | exon | g12835.t1.exon4 | 26473927 | 26473990 |
| chr_1 | g12835 | g12835.t1 | cds | g12835.t1.CDS4 | 26473927 | 26473990 |
| chr_1 | g12835 | g12835.t1 | exon | g12835.t1.exon5 | 26474355 | 26474416 |
| chr_1 | g12835 | g12835.t1 | cds | g12835.t1.CDS5 | 26474355 | 26474416 |
| chr_1 | g12835 | g12835.t1 | exon | g12835.t1.exon6 | 26474478 | 26474493 |
| chr_1 | g12835 | g12835.t1 | cds | g12835.t1.CDS6 | 26474478 | 26474493 |
| chr_1 | g12835 | g12835.t1 | TSS | g12835.t1 | 26474672 | 26474672 |
Sequences
>g12835.t1 Gene=g12835 Length=756
ATGGAGGAGGCAAAAGGCAACAACTCAGTCCTTAATCATAAGAAACTCATGCACGACATG
TATCAAGATTTATCAGAGGAACATCCTAGAAAATTAATCCCAGATCTTTGCAAACAATTC
TATGATCTAGGATGGGTTACCGGTACTGGTGGGGGTATTTCTATCAAATTAGACGATGAA
ATTTATATTGCGCCTTCTGGTGTTCAAAAAGAAAGAATTCAAATTGATGATTTATTTATT
CAAAATTTGGATGGTGATGATTTGGTCACACCACCTGATTATAAAAAATTGAAAAAATCT
CAATGTACACCACTCTTCATGATCGCGTATAAAATGCGAAATGCAGGCTCTGTAATTCAT
ACTCACTCACCTAATGCAGTTATGGCTACATTGCTTTATGAAAAAGAATTTAAAATAACT
CATCAAGAAATGATTAAGGGAATTTTCGATTACGAATTAAATCGTTATTTGAGATATGAT
GAGGAACTTGTAGTTCCGATCATTGAAAATACAAATCAAGAGAGAGACTTGGAAGAGAGC
TCATATAACGCAATAAAGGAATATCCAGGAACGTCTGCCGTTCTAGTAAGACGTCATGGC
ATTTATGTTTGGGGAAAATCATGGCAATCAGCAAAAACACAATGTGAATGTTATGACTAT
TTATTCAATATTGCTCTTGAAATGAAAAAATTTGGTCTAGATCCAAGCGCCATACCATCA
TCTAATTCTTCTCAAACAAAAACCAACAAAAAATAA
>g12835.t1 Gene=g12835 Length=251
MEEAKGNNSVLNHKKLMHDMYQDLSEEHPRKLIPDLCKQFYDLGWVTGTGGGISIKLDDE
IYIAPSGVQKERIQIDDLFIQNLDGDDLVTPPDYKKLKKSQCTPLFMIAYKMRNAGSVIH
THSPNAVMATLLYEKEFKITHQEMIKGIFDYELNRYLRYDEELVVPIIENTNQERDLEES
SYNAIKEYPGTSAVLVRRHGIYVWGKSWQSAKTQCECYDYLFNIALEMKKFGLDPSAIPS
SNSSQTKTNKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12835.t1 | Gene3D | G3DSA:3.40.225.10 | - | 24 | 246 | 0.00000 |
| 3 | g12835.t1 | Hamap | MF_03116 | Methylthioribulose-1-phosphate dehydratase [APIP]. | 18 | 234 | 45.41258 |
| 2 | g12835.t1 | PANTHER | PTHR10640 | METHYLTHIORIBULOSE-1-PHOSPHATE DEHYDRATASE | 21 | 244 | 0.00000 |
| 1 | g12835.t1 | Pfam | PF00596 | Class II Aldolase and Adducin N-terminal domain | 33 | 226 | 0.00000 |
| 5 | g12835.t1 | SMART | SM01007 | Aldolase_II_2 | 31 | 226 | 0.00000 |
| 4 | g12835.t1 | SUPERFAMILY | SSF53639 | AraD/HMP-PK domain-like | 26 | 240 | 0.00000 |
| 7 | g12835.t1 | TIGRFAM | TIGR03328 | salvage_mtnB: methylthioribulose-1-phosphate dehydratase | 34 | 231 | 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:0046872 | metal ion binding | MF |
| GO:0019509 | L-methionine salvage from methylthioadenosine | BP |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
- This transcript has been annotated with K08964 (methylthioribulose-1-phosphate dehydratase)
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.
