Gene loci information

Transcript annotation

  • This transcript has been annotated as Trehalose-6-phosphate phosphatase.

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 g13300 g13300.t60 TSS g13300.t60 29008120 29008120
chr_1 g13300 g13300.t60 isoform g13300.t60 29008186 29009204
chr_1 g13300 g13300.t60 exon g13300.t60.exon1 29008186 29008530
chr_1 g13300 g13300.t60 cds g13300.t60.CDS1 29008247 29008530
chr_1 g13300 g13300.t60 exon g13300.t60.exon2 29008591 29008720
chr_1 g13300 g13300.t60 cds g13300.t60.CDS2 29008591 29008720
chr_1 g13300 g13300.t60 exon g13300.t60.exon3 29008763 29008906
chr_1 g13300 g13300.t60 cds g13300.t60.CDS3 29008763 29008906
chr_1 g13300 g13300.t60 exon g13300.t60.exon4 29008971 29009004
chr_1 g13300 g13300.t60 cds g13300.t60.CDS4 29008971 29009004
chr_1 g13300 g13300.t60 exon g13300.t60.exon5 29009056 29009204
chr_1 g13300 g13300.t60 cds g13300.t60.CDS5 29009056 29009204
chr_1 g13300 g13300.t60 TTS g13300.t60 29009276 29009276

Sequences

>g13300.t60 Gene=g13300 Length=802
AGTCTTCGTTGTGAGTGCATTGAGAATTGTCGAACAATTAGATTTGAAACTTGAGCCACA
AATGGAAGATTTAGAAAAATACTTGGAGGATTATGTGTCGAATAAACCATTCGCGTTATT
ACTCGATTATGACGGCACGTTGGCTGCCATTCAACCACATCCAAATATGACATACATGAC
TGAATATACCAAAGAAGCGCTATTGAACATCTCATCTTACCCCAACGTGTATTTAGCAGT
TATATCCGGAAGGGGAGTTGATGATGTGAAGACAAAAGTTGGTATCGATGGAATTGTTTA
TGCTGGAAATCATGGTCTCGAAATTTTATATCCTAATGGAACTCGTTACATACACGAAGT
TCCAAGTGATGTTAAAGCAAATTTTACAAAAATGGTGGAAGCTTTAGAAAATCTTAAAAG
AGACGGAAGTTGGGTCGAAAATAAGAAATTCTCAGTAACTTTTCACTTTAGAGCTGAAAT
TATCGAGAAATTTGGATATCGAGCAAATCCAGCTCATTGCGCTATTGAAGCAAAACCACC
GGTAGTATGGCATAAGGGCAAGGCAGCCGAATATATTTTAAATCACTCATTTGGTAAAGA
TTGGAGAGAAAAAATTCAAGTTGTGTTTGCTGGCGATGATACAACCGATGAAGATGTTTT
CGAGTTACTTCAAGGAATTGGTGTTACTTTTAGAGTCACAAAGGATCCAAACATTGTGAC
TAAAGCAACTTACAAAGTGCCATCAACTGAAGCTGTTACAAAGGTTCTACAATGGGTCGA
TAAAAAATTTGGAAATAAATAA

>g13300.t60 Gene=g13300 Length=246
MEDLEKYLEDYVSNKPFALLLDYDGTLAAIQPHPNMTYMTEYTKEALLNISSYPNVYLAV
ISGRGVDDVKTKVGIDGIVYAGNHGLEILYPNGTRYIHEVPSDVKANFTKMVEALENLKR
DGSWVENKKFSVTFHFRAEIIEKFGYRANPAHCAIEAKPPVVWHKGKAAEYILNHSFGKD
WREKIQVVFAGDDTTDEDVFELLQGIGVTFRVTKDPNIVTKATYKVPSTEAVTKVLQWVD
KKFGNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13300.t60 CDD cd01627 HAD_TPP 18 232 0
6 g13300.t60 Gene3D G3DSA:3.40.50.1000 - 19 226 0
7 g13300.t60 Gene3D G3DSA:3.30.70.1020 - 101 160 0
3 g13300.t60 PANTHER PTHR43768 TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 237 0
4 g13300.t60 PANTHER PTHR43768:SF3 TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 237 0
1 g13300.t60 Pfam PF02358 Trehalose-phosphatase 20 137 0
2 g13300.t60 Pfam PF02358 Trehalose-phosphatase 143 226 0
5 g13300.t60 SUPERFAMILY SSF56784 HAD-like 18 239 0
8 g13300.t60 TIGRFAM TIGR00685 T6PP: trehalose-phosphatase 18 138 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:0005992 trehalose biosynthetic process BP
GO:0003824 catalytic 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