Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t6 isoform g13509.t6 30575255 30583540
chr_1 g13509 g13509.t6 exon g13509.t6.exon1 30575255 30575331
chr_1 g13509 g13509.t6 cds g13509.t6.CDS1 30575255 30575331
chr_1 g13509 g13509.t6 exon g13509.t6.exon2 30579764 30579975
chr_1 g13509 g13509.t6 cds g13509.t6.CDS2 30579764 30579975
chr_1 g13509 g13509.t6 exon g13509.t6.exon3 30582937 30583540
chr_1 g13509 g13509.t6 cds g13509.t6.CDS3 30582937 30583241
chr_1 g13509 g13509.t6 TTS g13509.t6 30584495 30584495
chr_1 g13509 g13509.t6 TSS g13509.t6 NA NA

Sequences

>g13509.t6 Gene=g13509 Length=893
ATGTTGCTCCTTTCATTTCCAAAATCAATCGGATTAATCGGCTCTGTCCTTGCATTACGC
TTGATTGCAACAACTGGAGTAATGGCAACTGAATTGAAGCAAGGAAATCCTGATCAAGCA
AAATCGGTCTATGAGTTTGTCGTTAATGATATCAAGGGCAATCCAATCAGCATGGAAAAG
TACCGTGGCCATCCATTGATCATTGTCAACGTTGCATCTAAATGTGGATATACCGAAAAG
CATTATGCTGAATTGAATGCACTCTACGATGAATATGCCGAATCAAAGGGTTTACGTATT
CTTGCATTCCCATGTAGTCAATTTAGCATAGGAGAAGCTACTCCTGATGAACTTCAGGGA
TGTATAAAGGCTCATAACGTTAAATTTGATGTTTTTGAACATGTTAAAGTTAATGGCGAT
GATGCTCATCCATTATGGCAGTATTTGAAAAAACAACAAGGTGGAACAATTATTGATGCA
ATTAAATGGGATTATACTAAATTTATTGTTGACAAAAATGGCGTACCAGTTGACCGTTTT
GCTCCAACTACTGATCCATTAGAAATGATTGCAGATCTTAAGAAATACTTGTAAAGAGTA
GATTTTTATATTGCAAACTCTGCCTTATTTTACGAGTTACTTTAAATTTTTCATTCATCT
TGAAAAAATAATAGTTGTTTAAGATCATCATTCCAGTTATTTATAACGACGTTGACGGTT
GAATTTTATATTAATTAACTTGGCATATGACGACAAATTTTTATACTCTTTATCTCTCTT
ACATGTAATGAAATATTCTCAAAATTTCTATAAATAATCCTTTTATTCTCTAATAATATG
TTTTTTTCACAATATTATGAAATGAATAAAGTGCAGGCATAAAAATATTCTTC

>g13509.t6 Gene=g13509 Length=197
MLLLSFPKSIGLIGSVLALRLIATTGVMATELKQGNPDQAKSVYEFVVNDIKGNPISMEK
YRGHPLIIVNVASKCGYTEKHYAELNALYDEYAESKGLRILAFPCSQFSIGEATPDELQG
CIKAHNVKFDVFEHVKVNGDDAHPLWQYLKKQQGGTIIDAIKWDYTKFIVDKNGVPVDRF
APTTDPLEMIADLKKYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g13509.t6 CDD cd00340 GSH_Peroxidase 42 193 5.99913E-74
9 g13509.t6 Gene3D G3DSA:3.40.30.10 Glutaredoxin 30 197 4.1E-57
2 g13509.t6 PANTHER PTHR11592:SF121 GLUTATHIONE PEROXIDASE 27 197 3.5E-71
3 g13509.t6 PANTHER PTHR11592 GLUTATHIONE PEROXIDASE 27 197 3.5E-71
15 g13509.t6 PIRSF PIRSF000303 Glutathion_perox 16 197 2.8E-58
4 g13509.t6 PRINTS PR01011 Glutathione peroxidase family signature 61 78 1.0E-13
6 g13509.t6 PRINTS PR01011 Glutathione peroxidase family signature 98 114 1.0E-13
5 g13509.t6 PRINTS PR01011 Glutathione peroxidase family signature 161 170 1.0E-13
1 g13509.t6 Pfam PF00255 Glutathione peroxidase 43 150 2.9E-32
11 g13509.t6 Phobius SIGNAL_PEPTIDE Signal peptide region 1 29 -
12 g13509.t6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 9 -
13 g13509.t6 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 10 21 -
14 g13509.t6 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 22 29 -
10 g13509.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 197 -
17 g13509.t6 ProSitePatterns PS00460 Glutathione peroxidases active site. 63 78 -
18 g13509.t6 ProSiteProfiles PS51355 Glutathione peroxidase profile. 33 197 58.817
7 g13509.t6 SUPERFAMILY SSF52833 Thioredoxin-like 41 197 8.05E-47
8 g13509.t6 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 29 -

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. There were no conditions that were differentially expressed