Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t34 TTS g12835.t34 26473084 26473084
chr_1 g12835 g12835.t34 isoform g12835.t34 26473115 26474493
chr_1 g12835 g12835.t34 exon g12835.t34.exon1 26473115 26473432
chr_1 g12835 g12835.t34 cds g12835.t34.CDS1 26473115 26473432
chr_1 g12835 g12835.t34 exon g12835.t34.exon2 26473499 26473672
chr_1 g12835 g12835.t34 cds g12835.t34.CDS2 26473499 26473603
chr_1 g12835 g12835.t34 exon g12835.t34.exon3 26473729 26474416
chr_1 g12835 g12835.t34 exon g12835.t34.exon4 26474478 26474493
chr_1 g12835 g12835.t34 TSS g12835.t34 26474672 26474672

Sequences

>g12835.t34 Gene=g12835 Length=1196
ATGGAGGAGGCAAAAGGCAACAACTCAGTCCTTAATCATAAGAAACTCATGCACGACATG
TATCAAGATTTATCAGAGGTGAGTTAAAATATTTAATTTCATTAATGAATGTTTCCAAAA
TCGATTTTGGAAAAAAATGCATAAAATAAATGTCGATAGTATAGAACAGTGATCATAAAA
ATTTCATGCGTGATTAGTAATTCATTCGTTCTTACTATTTGACTTTGTGGATTTAGAAAA
AATGAATAAAGATTTTACTGTGACTAAACCAGCGGTAAGTAGCAAAGTTTGTTATCCATA
GTGTTTTAACACATTAAAATTTATCAATATTTTATGAAAATCATGCAGAAATTTGAGGAT
TAAAACTGAATTACCTTTGTCATTTAATTTGACATACCTAATCAATTTTTTCTTACATAT
ATATTTTTCTTTTACAATTTAGGAACATCCTAGAAAATTAATCCCAGATCTTTGCAAACA
ATTCTATGATCTAGGATGGGTTACCGGTAAAATATTGAATTATCGATTTCATGATTACAT
TAATAATTAATGTTGACACTATTTTATTGTTTGATTATTAAGGTACTGGTGGGGGTATTT
CTATCAAATTAGACGATGAAATTTATATTGCGCCTTCTGGTGTTCAAAAAGAAAGAATTC
AAATTGATGATTTATTTATTCAAAATTTGGATGGTGATGATTTGGTCACACCACCTGATT
ATAAAAAATTGAAAAAATCTCAATGTACACCACTCTTCATGATCGCGTATAAAATGCGAA
ATGCAGGCTCTGTAATTCATACTCACTCACCTAATGCAGTTATGGCTACATTGCTTTATG
AAAAAGAATTTAAAATAACTCATCAAGAAATGATTAAGGGAATTTTCGATTACGAATTAA
ATCGTTATTTGAGATATGATGAGGAACTTGTAGTTCCGATCATTGAAAATACAAATCAAG
AGAGAGACTTGGAAGAGAGCTCATATAACGCAATAAAGGAATATCCAGGAACGTCTGCCG
TTCTAGTAAGACGTCATGGCATTTATGTTTGGGGAAAATCATGGCAATCAGCAAAAACAC
AATGTGAATGTTATGACTATTTATTCAATATTGCTCTTGAAATGAAAAAATTTGGTCTAG
ATCCAAGCGCCATACCATCATCTAATTCTTCTCAAACAAAAACCAACAAAAAATAA

>g12835.t34 Gene=g12835 Length=140
MRNAGSVIHTHSPNAVMATLLYEKEFKITHQEMIKGIFDYELNRYLRYDEELVVPIIENT
NQERDLEESSYNAIKEYPGTSAVLVRRHGIYVWGKSWQSAKTQCECYDYLFNIALEMKKF
GLDPSAIPSSNSSQTKTNKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g12835.t34 Gene3D G3DSA:3.40.225.10 - 1 135 0
2 g12835.t34 PANTHER PTHR10640 METHYLTHIORIBULOSE-1-PHOSPHATE DEHYDRATASE 1 133 0
1 g12835.t34 Pfam PF00596 Class II Aldolase and Adducin N-terminal domain 2 115 0
3 g12835.t34 SUPERFAMILY SSF53639 AraD/HMP-PK domain-like 3 129 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. There were no conditions that were differentially expressed