Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Extracellular superoxide dismutase [Cu-Zn].

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 g13490 g13490.t18 TTS g13490.t18 30456617 30456617
chr_1 g13490 g13490.t18 isoform g13490.t18 30456647 30458295
chr_1 g13490 g13490.t18 exon g13490.t18.exon1 30456647 30457129
chr_1 g13490 g13490.t18 cds g13490.t18.CDS1 30457118 30457129
chr_1 g13490 g13490.t18 exon g13490.t18.exon2 30457203 30457251
chr_1 g13490 g13490.t18 cds g13490.t18.CDS2 30457203 30457251
chr_1 g13490 g13490.t18 exon g13490.t18.exon3 30457522 30457803
chr_1 g13490 g13490.t18 cds g13490.t18.CDS3 30457522 30457803
chr_1 g13490 g13490.t18 exon g13490.t18.exon4 30457858 30457881
chr_1 g13490 g13490.t18 cds g13490.t18.CDS4 30457858 30457881
chr_1 g13490 g13490.t18 exon g13490.t18.exon5 30457941 30458295
chr_1 g13490 g13490.t18 cds g13490.t18.CDS5 30457941 30458068
chr_1 g13490 g13490.t18 TSS g13490.t18 NA NA

Sequences

>g13490.t18 Gene=g13490 Length=1193
ATGAAATCCTTAGTCATCATTTTCGTAATTTGTCTCTCAACAATCATCGTCAATGGCGAT
GAAGCGAAGCCTGCAAAAGCTATAGCAGTGCTTGGATTCTCAAACTCCGTCCATGGAAGT
AAGTTTTTTTTGGGTTCCGCTCGTTCAATCCTCAAATTGGCAGTAAAATTAGATGAGGAA
AAAACTTTTGTTGTTGTTGTTGTCGTTATGTGTAAAAAACCCTTTTTATGTGTTATTTTT
CCTTTTCTTTCTTAGACATCACTTTCTCACAATCATCCTGTACGGAAGCAGTTCTCGTTC
AAATTGAAATAACTGGCCTTACACCAGGCAAACACGGCTTTCATGTTCACGAAAAAGGCG
ATTTGTCGAATGGATGCACGAGCACAGGAAGTCATTTCAACCCAGATCGCTTGAATCATG
GCGCACGTGAAGCACAAGTTCGTCACGTTGGTGATTTGGGCAACGTTGTTGCTGATGATC
AAGGACGCGTCTCAACATCATTTTCGGATAATGTCATTACATTGTTTGGTGCTCGAAGTA
TCATTGGTAGAGCAATTGTTGTTCACACCGATGAAGATGACCTTGGTCTTACCGATCATC
AAGACTCTCATAAAACGGGAAATGCTGGTGGACGTGTTGCATGCGGAATTATTGGAATCT
TGGAGCCATCGAATGACGAATGGACATGTAATTCATCATCGAGAACACAACATACTCGCT
AATTCTAATGTTCGTTGTTGCTGTTATTGTTTGTGAAATGGAATTAAAGACAACTCATAC
ACACACTCTGACACACACAGTCTTGTTGACCATTTGACACATTTTTATCATGAATATTCT
TGTATTTGAATGAATATTTTGATTTATTAAAGTTGAAACTTGAAAACTCTTTTATACTCA
CAATTTTTATTGTTTATTTATTTCTTGGTTTATATTTTTGATTTTTATAGACCTGATTAT
TTGTTTATTAATGAATTAAACTATAAACTCACTTTAAAACAATCTAAATAGTAAAATTCA
AAAAAGCAGTTAAGATCAATTTTATTCACAATAAATTAATTTTGAGTGTAAATTTTCGAC
TAAAATTTTTCGTCGAGATTTAAATTATTCGGTCAGATTAAAAATAAATCTTTCCAAAAT
AAATCGTAAGATTTGAGAATTAAATTTTTTTAAGAAAAAAATAAAATTGGACA

>g13490.t18 Gene=g13490 Length=164
MCYFSFSFLDITFSQSSCTEAVLVQIEITGLTPGKHGFHVHEKGDLSNGCTSTGSHFNPD
RLNHGAREAQVRHVGDLGNVVADDQGRVSTSFSDNVITLFGARSIIGRAIVVHTDEDDLG
LTDHQDSHKTGNAGGRVACGIIGILEPSNDEWTCNSSSRTQHTR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g13490.t18 CDD cd00305 Cu-Zn_Superoxide_Dismutase 11 139 1.63122E-56
11 g13490.t18 Gene3D G3DSA:2.60.40.200 - 10 145 3.3E-55
2 g13490.t18 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 11 146 9.8E-50
3 g13490.t18 PANTHER PTHR10003:SF31 SUPEROXIDE DISMUTASE [CU-ZN] 3 11 146 9.8E-50
7 g13490.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 37 59 5.7E-40
6 g13490.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 73 82 5.7E-40
5 g13490.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 92 114 5.7E-40
4 g13490.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 117 143 5.7E-40
1 g13490.t18 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 11 142 4.4E-45
10 g13490.t18 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 37 47 -
9 g13490.t18 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 131 142 -
8 g13490.t18 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 11 145 4.58E-51

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:0006801 superoxide metabolic process BP
GO:0004784 superoxide dismutase activity MF
GO:0046872 metal ion binding 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