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.t24 isoform g13300.t24 29007929 29008900
chr_1 g13300 g13300.t24 exon g13300.t24.exon1 29007929 29007938
chr_1 g13300 g13300.t24 exon g13300.t24.exon2 29008121 29008530
chr_1 g13300 g13300.t24 cds g13300.t24.CDS1 29008145 29008530
chr_1 g13300 g13300.t24 exon g13300.t24.exon3 29008591 29008900
chr_1 g13300 g13300.t24 cds g13300.t24.CDS2 29008591 29008900
chr_1 g13300 g13300.t24 TTS g13300.t24 29009276 29009276
chr_1 g13300 g13300.t24 TSS g13300.t24 NA NA

Sequences

>g13300.t24 Gene=g13300 Length=730
TCTGTTTTTTATCACTCTCTGATAATAATAATTCATGACAATACTACACAAGCTAACTTT
AAATCTCATTTTCACAGTCTTCGTTGTGAGTGCATTGAGAATTGTCGAACAATTAGATTT
GAAACTTGAGCCACAAATGGAAGATTTAGAAAAATACTTGGAGGATTATGTGTCGAATAA
ACCATTCGCGTTATTACTCGATTATGACGGCACGTTGGCTGCCATTCAACCACATCCAAA
TATGACATACATGACTGAATATACCAAAGAAGCGCTATTGAACATCTCATCTTACCCCAA
CGTGTATTTAGCAGTTATATCCGGAAGGGGAGTTGATGATGTGAAGACAAAAGTTGGTAT
CGATGGAATTGTTTATGCTGGAAATCATGGTCTCGAAATTTTATATCCTAATGGAACTCG
TTACATACACGAAGTTCCAAGTGATGTTAAAGCAAATTTTACAAAAATGGTGGAAGCTTT
AGAAAATCTTAAAAGAGACGGAAGTTGGGTCGAAAATAAGAAATTCTCAGTAACTTTTCA
CTTTAGAGCTGTGCCTGAAAAAGATCATGAGAAAATCAACAATGAAGCTAAGGAAATTAT
CGAGAAATTTGGATATCGAGCAAATCCAGCTCATTGCGCTATTGAAGCAAAACCACCGGT
AGTATGGCATAAGGGCAAGGCAGCCGAATATATTTTAAATCACTCATTTGGTAAAGATTG
GAGAGAAAAA

>g13300.t24 Gene=g13300 Length=232
MTILHKLTLNLIFTVFVVSALRIVEQLDLKLEPQMEDLEKYLEDYVSNKPFALLLDYDGT
LAAIQPHPNMTYMTEYTKEALLNISSYPNVYLAVISGRGVDDVKTKVGIDGIVYAGNHGL
EILYPNGTRYIHEVPSDVKANFTKMVEALENLKRDGSWVENKKFSVTFHFRAVPEKDHEK
INNEAKEIIEKFGYRANPAHCAIEAKPPVVWHKGKAAEYILNHSFGKDWREK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g13300.t24 Gene3D G3DSA:3.40.50.1000 - 53 223 2.2E-28
7 g13300.t24 Gene3D G3DSA:3.30.70.1020 - 135 208 2.2E-28
2 g13300.t24 PANTHER PTHR43768 TREHALOSE 6-PHOSPHATE PHOSPHATASE 40 223 5.4E-37
3 g13300.t24 PANTHER PTHR43768:SF3 TREHALOSE 6-PHOSPHATE PHOSPHATASE 40 223 5.4E-37
1 g13300.t24 Pfam PF02358 Trehalose-phosphatase 54 227 7.7E-32
9 g13300.t24 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
10 g13300.t24 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
11 g13300.t24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 18 -
12 g13300.t24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 19 22 -
8 g13300.t24 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 232 -
4 g13300.t24 SUPERFAMILY SSF56784 HAD-like 52 223 1.61E-25
5 g13300.t24 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
15 g13300.t24 TIGRFAM TIGR00685 T6PP: trehalose-phosphatase 52 227 6.3E-32
14 g13300.t24 TIGRFAM TIGR01484 HAD-SF-IIB: HAD hydrolase, family IIB 53 225 4.7E-14
13 g13300.t24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 24 -

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

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.

Raw TPM values