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.t2 isoform g13300.t2 29007116 29009204
chr_1 g13300 g13300.t2 exon g13300.t2.exon1 29007116 29007341
chr_1 g13300 g13300.t2 exon g13300.t2.exon2 29008188 29008530
chr_1 g13300 g13300.t2 cds g13300.t2.CDS1 29008247 29008530
chr_1 g13300 g13300.t2 exon g13300.t2.exon3 29008591 29008906
chr_1 g13300 g13300.t2 cds g13300.t2.CDS2 29008591 29008906
chr_1 g13300 g13300.t2 exon g13300.t2.exon4 29008971 29009004
chr_1 g13300 g13300.t2 cds g13300.t2.CDS3 29008971 29009004
chr_1 g13300 g13300.t2 exon g13300.t2.exon5 29009056 29009204
chr_1 g13300 g13300.t2 cds g13300.t2.CDS4 29009056 29009204
chr_1 g13300 g13300.t2 TTS g13300.t2 29009276 29009276
chr_1 g13300 g13300.t2 TSS g13300.t2 NA NA

Sequences

>g13300.t2 Gene=g13300 Length=1068
AATAAACGTAAAATGACATATGATGCGAGAGAGCGAGAATTGAGTGTCAATAATTATTGA
CAGTTGATTAGCATATATGCAAATTTGCTGTCAATTAAGTATAGTTCAAAATTTTAAAAA
TAAAAATAGAAAGAAAGTGCATAGTGATAAAATAAAAATAGGTTTTGTCAGTTGTTATTG
ATTCCAATTCAATCAAATAGTTTATAAAATCTGTACAAGTCAAAAATCTTCGTTGTGAGT
GCATTGAGAATTGTCGAACAATTAGATTTGAAACTTGAGCCACAAATGGAAGATTTAGAA
AAATACTTGGAGGATTATGTGTCGAATAAACCATTCGCGTTATTACTCGATTATGACGGC
ACGTTGGCTGCCATTCAACCACATCCAAATATGACATACATGACTGAATATACCAAAGAA
GCGCTATTGAACATCTCATCTTACCCCAACGTGTATTTAGCAGTTATATCCGGAAGGGGA
GTTGATGATGTGAAGACAAAAGTTGGTATCGATGGAATTGTTTATGCTGGAAATCATGGT
CTCGAAATTTTATATCCTAATGGAACTCGTTACATACACGAAGTTCCAAGTGATGTTAAA
GCAAATTTTACAAAAATGGTGGAAGCTTTAGAAAATCTTAAAAGAGACGGAAGTTGGGTC
GAAAATAAGAAATTCTCAGTAACTTTTCACTTTAGAGCTGTGCCTGAAAAAGATCATGAG
AAAATCAACAATGAAGCTAAGGAAATTATCGAGAAATTTGGATATCGAGCAAATCCAGCT
CATTGCGCTATTGAAGCAAAACCACCGGTAGTATGGCATAAGGGCAAGGCAGCCGAATAT
ATTTTAAATCACTCATTTGGTAAAGATTGGAGAGAAAAAATTCAAGTTGTGTTTGCTGGC
GATGATACAACCGATGAAGATGTTTTCGAGTTACTTCAAGGAATTGGTGTTACTTTTAGA
GTCACAAAGGATCCAAACATTGTGACTAAAGCAACTTACAAAGTGCCATCAACTGAAGCT
GTTACAAAGGTTCTACAATGGGTCGATAAAAAATTTGGAAATAAATAA

>g13300.t2 Gene=g13300 Length=260
MEDLEKYLEDYVSNKPFALLLDYDGTLAAIQPHPNMTYMTEYTKEALLNISSYPNVYLAV
ISGRGVDDVKTKVGIDGIVYAGNHGLEILYPNGTRYIHEVPSDVKANFTKMVEALENLKR
DGSWVENKKFSVTFHFRAVPEKDHEKINNEAKEIIEKFGYRANPAHCAIEAKPPVVWHKG
KAAEYILNHSFGKDWREKIQVVFAGDDTTDEDVFELLQGIGVTFRVTKDPNIVTKATYKV
PSTEAVTKVLQWVDKKFGNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13300.t2 CDD cd01627 HAD_TPP 18 246 0
5 g13300.t2 Gene3D G3DSA:3.40.50.1000 - 19 240 0
6 g13300.t2 Gene3D G3DSA:3.30.70.1020 - 101 174 0
2 g13300.t2 PANTHER PTHR43768 TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 251 0
3 g13300.t2 PANTHER PTHR43768:SF3 TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 251 0
1 g13300.t2 Pfam PF02358 Trehalose-phosphatase 20 240 0
4 g13300.t2 SUPERFAMILY SSF56784 HAD-like 18 253 0
8 g13300.t2 TIGRFAM TIGR00685 T6PP: trehalose-phosphatase 18 253 0
7 g13300.t2 TIGRFAM TIGR01484 HAD-SF-IIB: HAD hydrolase, family IIB 19 222 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.

Raw TPM values