Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable methylthioribulose-1-phosphate dehydratase.

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 g12835 g12835.t39 TTS g12835.t39 26473084 26473084
chr_1 g12835 g12835.t39 isoform g12835.t39 26473115 26474493
chr_1 g12835 g12835.t39 exon g12835.t39.exon1 26473115 26473432
chr_1 g12835 g12835.t39 cds g12835.t39.CDS1 26473115 26473432
chr_1 g12835 g12835.t39 exon g12835.t39.exon2 26473499 26473672
chr_1 g12835 g12835.t39 cds g12835.t39.CDS2 26473499 26473672
chr_1 g12835 g12835.t39 exon g12835.t39.exon3 26473729 26473850
chr_1 g12835 g12835.t39 cds g12835.t39.CDS3 26473729 26473850
chr_1 g12835 g12835.t39 exon g12835.t39.exon4 26473927 26473990
chr_1 g12835 g12835.t39 cds g12835.t39.CDS4 26473927 26473990
chr_1 g12835 g12835.t39 exon g12835.t39.exon5 26474355 26474404
chr_1 g12835 g12835.t39 cds g12835.t39.CDS5 26474355 26474404
chr_1 g12835 g12835.t39 exon g12835.t39.exon6 26474478 26474493
chr_1 g12835 g12835.t39 cds g12835.t39.CDS6 26474478 26474493
chr_1 g12835 g12835.t39 TSS g12835.t39 26474672 26474672

Sequences

>g12835.t39 Gene=g12835 Length=744
ATGGAGGAGGCAAAAGTCCTTAATCATAAGAAACTCATGCACGACATGTATCAAGATTTA
TCAGAGGAACATCCTAGAAAATTAATCCCAGATCTTTGCAAACAATTCTATGATCTAGGA
TGGGTTACCGGTACTGGTGGGGGTATTTCTATCAAATTAGACGATGAAATTTATATTGCG
CCTTCTGGTGTTCAAAAAGAAAGAATTCAAATTGATGATTTATTTATTCAAAATTTGGAT
GGTGATGATTTGGTCACACCACCTGATTATAAAAAATTGAAAAAATCTCAATGTACACCA
CTCTTCATGATCGCGTATAAAATGCGAAATGCAGGCTCTGTAATTCATACTCACTCACCT
AATGCAGTTATGGCTACATTGCTTTATGAAAAAGAATTTAAAATAACTCATCAAGAAATG
ATTAAGGGAATTTTCGATTACGAATTAAATCGTTATTTGAGATATGATGAGGAACTTGTA
GTTCCGATCATTGAAAATACAAATCAAGAGAGAGACTTGGAAGAGAGCTCATATAACGCA
ATAAAGGAATATCCAGGAACGTCTGCCGTTCTAGTAAGACGTCATGGCATTTATGTTTGG
GGAAAATCATGGCAATCAGCAAAAACACAATGTGAATGTTATGACTATTTATTCAATATT
GCTCTTGAAATGAAAAAATTTGGTCTAGATCCAAGCGCCATACCATCATCTAATTCTTCT
CAAACAAAAACCAACAAAAAATAA

>g12835.t39 Gene=g12835 Length=247
MEEAKVLNHKKLMHDMYQDLSEEHPRKLIPDLCKQFYDLGWVTGTGGGISIKLDDEIYIA
PSGVQKERIQIDDLFIQNLDGDDLVTPPDYKKLKKSQCTPLFMIAYKMRNAGSVIHTHSP
NAVMATLLYEKEFKITHQEMIKGIFDYELNRYLRYDEELVVPIIENTNQERDLEESSYNA
IKEYPGTSAVLVRRHGIYVWGKSWQSAKTQCECYDYLFNIALEMKKFGLDPSAIPSSNSS
QTKTNKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g12835.t39 Gene3D G3DSA:3.40.225.10 - 20 242 0.00000
3 g12835.t39 Hamap MF_03116 Methylthioribulose-1-phosphate dehydratase [APIP]. 14 230 45.41258
2 g12835.t39 PANTHER PTHR10640 METHYLTHIORIBULOSE-1-PHOSPHATE DEHYDRATASE 17 240 0.00000
1 g12835.t39 Pfam PF00596 Class II Aldolase and Adducin N-terminal domain 29 222 0.00000
5 g12835.t39 SMART SM01007 Aldolase_II_2 27 222 0.00000
4 g12835.t39 SUPERFAMILY SSF53639 AraD/HMP-PK domain-like 22 236 0.00000
7 g12835.t39 TIGRFAM TIGR03328 salvage_mtnB: methylthioribulose-1-phosphate dehydratase 30 227 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

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