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.t18 isoform g13300.t18 29007914 29009204
chr_1 g13300 g13300.t18 exon g13300.t18.exon1 29007914 29007941
chr_1 g13300 g13300.t18 exon g13300.t18.exon2 29008121 29008228
chr_1 g13300 g13300.t18 cds g13300.t18.CDS1 29008145 29008228
chr_1 g13300 g13300.t18 exon g13300.t18.exon3 29008310 29008530
chr_1 g13300 g13300.t18 cds g13300.t18.CDS2 29008310 29008530
chr_1 g13300 g13300.t18 exon g13300.t18.exon4 29008591 29008906
chr_1 g13300 g13300.t18 cds g13300.t18.CDS3 29008591 29008906
chr_1 g13300 g13300.t18 exon g13300.t18.exon5 29008971 29009004
chr_1 g13300 g13300.t18 cds g13300.t18.CDS4 29008971 29009004
chr_1 g13300 g13300.t18 exon g13300.t18.exon6 29009056 29009204
chr_1 g13300 g13300.t18 cds g13300.t18.CDS5 29009056 29009204
chr_1 g13300 g13300.t18 TTS g13300.t18 29009276 29009276
chr_1 g13300 g13300.t18 TSS g13300.t18 NA NA

Sequences

>g13300.t18 Gene=g13300 Length=856
ACTATTATATTTCTTTCTGTTTTTTGTGATCACTCTCTGATAATAATAATTCATGACAAT
ACTACACAAGCTAACTTTAAATCTCATTTTCACAGTCTTCGTTGTGAGTGCATTGAGAAT
TGTCGAACAATTAGATGATTATGACGGCACGTTGGCTGCCATTCAACCACATCCAAATAT
GACATACATGACTGAATATACCAAAGAAGCGCTATTGAACATCTCATCTTACCCCAACGT
GTATTTAGCAGTTATATCCGGAAGGGGAGTTGATGATGTGAAGACAAAAGTTGGTATCGA
TGGAATTGTTTATGCTGGAAATCATGGTCTCGAAATTTTATATCCTAATGGAACTCGTTA
CATACACGAAGTTCCAAGTGATGTTAAAGCAAATTTTACAAAAATGGTGGAAGCTTTAGA
AAATCTTAAAAGAGACGGAAGTTGGGTCGAAAATAAGAAATTCTCAGTAACTTTTCACTT
TAGAGCTGTGCCTGAAAAAGATCATGAGAAAATCAACAATGAAGCTAAGGAAATTATCGA
GAAATTTGGATATCGAGCAAATCCAGCTCATTGCGCTATTGAAGCAAAACCACCGGTAGT
ATGGCATAAGGGCAAGGCAGCCGAATATATTTTAAATCACTCATTTGGTAAAGATTGGAG
AGAAAAAATTCAAGTTGTGTTTGCTGGCGATGATACAACCGATGAAGATGTTTTCGAGTT
ACTTCAAGGAATTGGTGTTACTTTTAGAGTCACAAAGGATCCAAACATTGTGACTAAAGC
AACTTACAAAGTGCCATCAACTGAAGCTGTTACAAAGGTTCTACAATGGGTCGATAAAAA
ATTTGGAAATAAATAA

>g13300.t18 Gene=g13300 Length=267
MTILHKLTLNLIFTVFVVSALRIVEQLDDYDGTLAAIQPHPNMTYMTEYTKEALLNISSY
PNVYLAVISGRGVDDVKTKVGIDGIVYAGNHGLEILYPNGTRYIHEVPSDVKANFTKMVE
ALENLKRDGSWVENKKFSVTFHFRAVPEKDHEKINNEAKEIIEKFGYRANPAHCAIEAKP
PVVWHKGKAAEYILNHSFGKDWREKIQVVFAGDDTTDEDVFELLQGIGVTFRVTKDPNIV
TKATYKVPSTEAVTKVLQWVDKKFGNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g13300.t18 CDD cd01627 HAD_TPP 29 253 1.17838E-56
6 g13300.t18 Gene3D G3DSA:3.40.50.1000 - 29 247 7.6E-39
7 g13300.t18 Gene3D G3DSA:3.30.70.1020 - 108 181 7.6E-39
2 g13300.t18 PANTHER PTHR43768 TREHALOSE 6-PHOSPHATE PHOSPHATASE 29 258 2.8E-46
3 g13300.t18 PANTHER PTHR43768:SF3 TREHALOSE 6-PHOSPHATE PHOSPHATASE 29 258 2.8E-46
1 g13300.t18 Pfam PF02358 Trehalose-phosphatase 29 247 9.5E-39
9 g13300.t18 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
10 g13300.t18 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
11 g13300.t18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 18 -
12 g13300.t18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 19 22 -
8 g13300.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 267 -
4 g13300.t18 SUPERFAMILY SSF56784 HAD-like 29 260 2.17E-34
5 g13300.t18 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
16 g13300.t18 TIGRFAM TIGR00685 T6PP: trehalose-phosphatase 27 260 4.4E-41
15 g13300.t18 TIGRFAM TIGR01484 HAD-SF-IIB: HAD hydrolase, family IIB 29 229 4.1E-19
14 g13300.t18 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

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