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.t5 isoform g13509.t5 30575255 30583536
chr_1 g13509 g13509.t5 exon g13509.t5.exon1 30575255 30575316
chr_1 g13509 g13509.t5 cds g13509.t5.CDS1 30575255 30575316
chr_1 g13509 g13509.t5 exon g13509.t5.exon2 30579764 30579975
chr_1 g13509 g13509.t5 cds g13509.t5.CDS2 30579764 30579975
chr_1 g13509 g13509.t5 exon g13509.t5.exon3 30582937 30583536
chr_1 g13509 g13509.t5 cds g13509.t5.CDS3 30582937 30583241
chr_1 g13509 g13509.t5 TTS g13509.t5 30584495 30584495
chr_1 g13509 g13509.t5 TSS g13509.t5 NA NA

Sequences

>g13509.t5 Gene=g13509 Length=874
ATGTTGCTCCTTTCATTTCCAAAATCAATCGGATTAATCGGCTCTGTCCTTGCATTACGC
TTAGTAATGGCAACTGAATTGAAGCAAGGAAATCCTGATCAAGCAAAATCGGTCTATGAG
TTTGTCGTTAATGATATCAAGGGCAATCCAATCAGCATGGAAAAGTACCGTGGCCATCCA
TTGATCATTGTCAACGTTGCATCTAAATGTGGATATACCGAAAAGCATTATGCTGAATTG
AATGCACTCTACGATGAATATGCCGAATCAAAGGGTTTACGTATTCTTGCATTCCCATGT
AGTCAATTTAGCATAGGAGAAGCTACTCCTGATGAACTTCAGGGATGTATAAAGGCTCAT
AACGTTAAATTTGATGTTTTTGAACATGTTAAAGTTAATGGCGATGATGCTCATCCATTA
TGGCAGTATTTGAAAAAACAACAAGGTGGAACAATTATTGATGCAATTAAATGGGATTAT
ACTAAATTTATTGTTGACAAAAATGGCGTACCAGTTGACCGTTTTGCTCCAACTACTGAT
CCATTAGAAATGATTGCAGATCTTAAGAAATACTTGTAAAGAGTAGATTTTTATATTGCA
AACTCTGCCTTATTTTACGAGTTACTTTAAATTTTTCATTCATCTTGAAAAAATAATAGT
TGTTTAAGATCATCATTCCAGTTATTTATAACGACGTTGACGGTTGAATTTTATATTAAT
TAACTTGGCATATGACGACAAATTTTTATACTCTTTATCTCTCTTACATGTAATGAAATA
TTCTCAAAATTTCTATAAATAATCCTTTTATTCTCTAATAATATGTTTTTTTCACAATAT
TATGAAATGAATAAAGTGCAGGCATAAAAATATT

>g13509.t5 Gene=g13509 Length=192
MLLLSFPKSIGLIGSVLALRLVMATELKQGNPDQAKSVYEFVVNDIKGNPISMEKYRGHP
LIIVNVASKCGYTEKHYAELNALYDEYAESKGLRILAFPCSQFSIGEATPDELQGCIKAH
NVKFDVFEHVKVNGDDAHPLWQYLKKQQGGTIIDAIKWDYTKFIVDKNGVPVDRFAPTTD
PLEMIADLKKYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g13509.t5 CDD cd00340 GSH_Peroxidase 37 188 8.67734E-74
9 g13509.t5 Gene3D G3DSA:3.40.30.10 Glutaredoxin 25 192 3.7E-57
2 g13509.t5 PANTHER PTHR11592:SF121 GLUTATHIONE PEROXIDASE 25 192 5.8E-71
3 g13509.t5 PANTHER PTHR11592 GLUTATHIONE PEROXIDASE 25 192 5.8E-71
15 g13509.t5 PIRSF PIRSF000303 Glutathion_perox 13 192 3.5E-58
6 g13509.t5 PRINTS PR01011 Glutathione peroxidase family signature 56 73 9.8E-14
5 g13509.t5 PRINTS PR01011 Glutathione peroxidase family signature 93 109 9.8E-14
4 g13509.t5 PRINTS PR01011 Glutathione peroxidase family signature 156 165 9.8E-14
1 g13509.t5 Pfam PF00255 Glutathione peroxidase 38 145 2.7E-32
11 g13509.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 24 -
12 g13509.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 8 -
13 g13509.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 9 19 -
14 g13509.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 20 24 -
10 g13509.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 25 192 -
17 g13509.t5 ProSitePatterns PS00460 Glutathione peroxidases active site. 58 73 -
18 g13509.t5 ProSiteProfiles PS51355 Glutathione peroxidase profile. 28 192 58.817
7 g13509.t5 SUPERFAMILY SSF52833 Thioredoxin-like 36 192 7.37E-47
8 g13509.t5 SignalP_EUK SignalP-noTM SignalP-noTM 1 18 -

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