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.t20 isoform g13300.t20 29007914 29009204
chr_1 g13300 g13300.t20 exon g13300.t20.exon1 29007914 29007941
chr_1 g13300 g13300.t20 exon g13300.t20.exon2 29008121 29008530
chr_1 g13300 g13300.t20 cds g13300.t20.CDS1 29008145 29008530
chr_1 g13300 g13300.t20 exon g13300.t20.exon3 29008591 29008906
chr_1 g13300 g13300.t20 cds g13300.t20.CDS2 29008591 29008906
chr_1 g13300 g13300.t20 exon g13300.t20.exon4 29008971 29009010
chr_1 g13300 g13300.t20 cds g13300.t20.CDS3 29008971 29009010
chr_1 g13300 g13300.t20 exon g13300.t20.exon5 29009056 29009204
chr_1 g13300 g13300.t20 cds g13300.t20.CDS4 29009056 29009204
chr_1 g13300 g13300.t20 TTS g13300.t20 29009276 29009276
chr_1 g13300 g13300.t20 TSS g13300.t20 NA NA

Sequences

>g13300.t20 Gene=g13300 Length=943
ACTATTATATTTCTTTCTGTTTTTTGTGATCACTCTCTGATAATAATAATTCATGACAAT
ACTACACAAGCTAACTTTAAATCTCATTTTCACAGTCTTCGTTGTGAGTGCATTGAGAAT
TGTCGAACAATTAGATTTGAAACTTGAGCCACAAATGGAAGATTTAGAAAAATACTTGGA
GGATTATGTGTCGAATAAACCATTCGCGTTATTACTCGATTATGACGGCACGTTGGCTGC
CATTCAACCACATCCAAATATGACATACATGACTGAATATACCAAAGAAGCGCTATTGAA
CATCTCATCTTACCCCAACGTGTATTTAGCAGTTATATCCGGAAGGGGAGTTGATGATGT
GAAGACAAAAGTTGGTATCGATGGAATTGTTTATGCTGGAAATCATGGTCTCGAAATTTT
ATATCCTAATGGAACTCGTTACATACACGAAGTTCCAAGTGATGTTAAAGCAAATTTTAC
AAAAATGGTGGAAGCTTTAGAAAATCTTAAAAGAGACGGAAGTTGGGTCGAAAATAAGAA
ATTCTCAGTAACTTTTCACTTTAGAGCTGTGCCTGAAAAAGATCATGAGAAAATCAACAA
TGAAGCTAAGGAAATTATCGAGAAATTTGGATATCGAGCAAATCCAGCTCATTGCGCTAT
TGAAGCAAAACCACCGGTAGTATGGCATAAGGGCAAGGCAGCCGAATATATTTTAAATCA
CTCATTTGGTAAAGATTGGAGAGAAAAAATTCAAGTTGTGTTTGCTGGCGATGATACAAC
CGATGAAGGTAAAGATGTTTTCGAGTTACTTCAAGGAATTGGTGTTACTTTTAGAGTCAC
AAAGGATCCAAACATTGTGACTAAAGCAACTTACAAAGTGCCATCAACTGAAGCTGTTAC
AAAGGTTCTACAATGGGTCGATAAAAAATTTGGAAATAAATAA

>g13300.t20 Gene=g13300 Length=296
MTILHKLTLNLIFTVFVVSALRIVEQLDLKLEPQMEDLEKYLEDYVSNKPFALLLDYDGT
LAAIQPHPNMTYMTEYTKEALLNISSYPNVYLAVISGRGVDDVKTKVGIDGIVYAGNHGL
EILYPNGTRYIHEVPSDVKANFTKMVEALENLKRDGSWVENKKFSVTFHFRAVPEKDHEK
INNEAKEIIEKFGYRANPAHCAIEAKPPVVWHKGKAAEYILNHSFGKDWREKIQVVFAGD
DTTDEGKDVFELLQGIGVTFRVTKDPNIVTKATYKVPSTEAVTKVLQWVDKKFGNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g13300.t20 CDD cd01627 HAD_TPP 52 282 1.14603E-56
6 g13300.t20 Gene3D G3DSA:3.40.50.1000 - 53 276 2.2E-37
7 g13300.t20 Gene3D G3DSA:3.30.70.1020 - 135 208 2.2E-37
2 g13300.t20 PANTHER PTHR43768 TREHALOSE 6-PHOSPHATE PHOSPHATASE 40 287 5.8E-47
3 g13300.t20 PANTHER PTHR43768:SF3 TREHALOSE 6-PHOSPHATE PHOSPHATASE 40 287 5.8E-47
1 g13300.t20 Pfam PF02358 Trehalose-phosphatase 54 278 2.2E-37
9 g13300.t20 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
10 g13300.t20 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
11 g13300.t20 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 18 -
12 g13300.t20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 19 22 -
8 g13300.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 296 -
4 g13300.t20 SUPERFAMILY SSF56784 HAD-like 52 289 1.35E-32
5 g13300.t20 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
16 g13300.t20 TIGRFAM TIGR00685 T6PP: trehalose-phosphatase 52 289 7.3E-40
15 g13300.t20 TIGRFAM TIGR01484 HAD-SF-IIB: HAD hydrolase, family IIB 53 245 1.2E-17
14 g13300.t20 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