Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Probable phospholipid hydroperoxide glutathione peroxidase.

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 g13509 g13509.t18 isoform g13509.t18 30579760 30584221
chr_1 g13509 g13509.t18 exon g13509.t18.exon1 30579760 30579975
chr_1 g13509 g13509.t18 TSS g13509.t18 30579763 30579763
chr_1 g13509 g13509.t18 cds g13509.t18.CDS1 30579768 30579975
chr_1 g13509 g13509.t18 exon g13509.t18.exon2 30582937 30582942
chr_1 g13509 g13509.t18 cds g13509.t18.CDS2 30582937 30582942
chr_1 g13509 g13509.t18 exon g13509.t18.exon3 30583923 30584221
chr_1 g13509 g13509.t18 cds g13509.t18.CDS3 30583923 30584221
chr_1 g13509 g13509.t18 TTS g13509.t18 30584495 30584495

Sequences

>g13509.t18 Gene=g13509 Length=521
GCAGAGTAATGGCAACTGAATTGAAGCAAGGAAATCCTGATCAAGCAAAATCGGTCTATG
AGTTTGTCGTTAATGATATCAAGGGCAATCCAATCAGCATGGAAAAGTACCGTGGCCATC
CATTGATCATTGTCAACGTTGCATCTAAATGTGGATATACCGAAAAGCATTATGCTGAAT
TGAATGCACTCTACGATGAATATGCCGAATCAAAGGGTTTACGTATTCTTGCATTCCCAT
GTGATCAATTTAGCGTAGGAGGAGCTACTCCTGATGAATTTCAGGCATGTTTGAAGGCTC
ATAACGTTAAATTTGATGTTTTCGGAACAGTTAAAGTTAATGGAGATGATGCTCATCCAT
TATGGAAATATTTGAAAAAACAACAGGATGGAACTTTGATTGATACAATTAAATGGGACT
ACACTAAATTTATTGTTGACAAAAATGGCAAACCAGTTGACCGTTTTGCTCCAACTACTG
ATCCATTGAAAATGATTGAAGATCTTAAGAAATATATGTAA

>g13509.t18 Gene=g13509 Length=170
MATELKQGNPDQAKSVYEFVVNDIKGNPISMEKYRGHPLIIVNVASKCGYTEKHYAELNA
LYDEYAESKGLRILAFPCDQFSVGGATPDEFQACLKAHNVKFDVFGTVKVNGDDAHPLWK
YLKKQQDGTLIDTIKWDYTKFIVDKNGKPVDRFAPTTDPLKMIEDLKKYM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13509.t18 CDD cd00340 GSH_Peroxidase 15 166 1.76656E-73
8 g13509.t18 Gene3D G3DSA:3.40.30.10 Glutaredoxin 4 170 1.7E-57
2 g13509.t18 PANTHER PTHR11592:SF121 GLUTATHIONE PEROXIDASE 6 169 4.1E-70
3 g13509.t18 PANTHER PTHR11592 GLUTATHIONE PEROXIDASE 6 169 4.1E-70
9 g13509.t18 PIRSF PIRSF000303 Glutathion_perox 1 170 4.1E-58
5 g13509.t18 PRINTS PR01011 Glutathione peroxidase family signature 34 51 8.1E-13
4 g13509.t18 PRINTS PR01011 Glutathione peroxidase family signature 71 87 8.1E-13
6 g13509.t18 PRINTS PR01011 Glutathione peroxidase family signature 134 143 8.1E-13
1 g13509.t18 Pfam PF00255 Glutathione peroxidase 16 123 6.5E-31
11 g13509.t18 ProSitePatterns PS00460 Glutathione peroxidases active site. 36 51 -
12 g13509.t18 ProSiteProfiles PS51355 Glutathione peroxidase profile. 6 170 57.62
7 g13509.t18 SUPERFAMILY SSF52833 Thioredoxin-like 14 169 1.75E-46

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:0006979 response to oxidative stress BP
GO:0004602 glutathione peroxidase activity MF
GO:0055114 NA NA

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