Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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_4 g16280 g16280.t25 TTS g16280.t25 8956500 8956500
chr_4 g16280 g16280.t25 isoform g16280.t25 8956673 8960025
chr_4 g16280 g16280.t25 exon g16280.t25.exon1 8956673 8956897
chr_4 g16280 g16280.t25 cds g16280.t25.CDS1 8956673 8956897
chr_4 g16280 g16280.t25 exon g16280.t25.exon2 8956961 8957070
chr_4 g16280 g16280.t25 cds g16280.t25.CDS2 8956961 8957070
chr_4 g16280 g16280.t25 exon g16280.t25.exon3 8957152 8957212
chr_4 g16280 g16280.t25 cds g16280.t25.CDS3 8957152 8957212
chr_4 g16280 g16280.t25 exon g16280.t25.exon4 8957356 8957465
chr_4 g16280 g16280.t25 cds g16280.t25.CDS4 8957356 8957463
chr_4 g16280 g16280.t25 TSS g16280.t25 8957532 8957532
chr_4 g16280 g16280.t25 exon g16280.t25.exon5 8959997 8960025

Sequences

>g16280.t25 Gene=g16280 Length=535
ATTACAGGTAGATCGTTCTCTGCGCTACATAATGGATAAGTTAAAAAAAGCATTAGATAT
TGAAAAAGATCATCCAGTTACAAGAGCTGTTTGTGTCATGATTGGTGAAGCTGAAGGAAC
TTGCTACTTTGAACAAGCTTCAAAGAAGGGTCCCGTTCATATCACTGGTGAAATCAAAGG
TTTAAAACCTGGCTTGCATGGTTTTCATATCCATGAATATGGTGACATTACCAACGGATG
TATGTCTGCCGGACAGCATTTCAATCCATACAACAAACAACATGGAGGAACTCTTGATGA
CAATCGTCATGTTGGTGATTTGGGAAATATTAAAGCTGAAGAAAATGGAATTGCAAAAAT
TGACATAACAGATCGAATGATTTCTCTGCATGGAAACTCGAATATTATTGGTCGCACGTT
GGTTGTACATGTAAATGCCGACGATTTGGGACTTGGGTCCAATGAACAATCAAAATCCGA
CGGTAACTCTGGTGGAAGAATTAGCTGTGGTGTTATTGGCATCTGCAAGGCATAA

>g16280.t25 Gene=g16280 Length=167
MDKLKKALDIEKDHPVTRAVCVMIGEAEGTCYFEQASKKGPVHITGEIKGLKPGLHGFHI
HEYGDITNGCMSAGQHFNPYNKQHGGTLDDNRHVGDLGNIKAEENGIAKIDITDRMISLH
GNSNIIGRTLVVHVNADDLGLGSNEQSKSDGNSGGRISCGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16280.t25 CDD cd00305 Cu-Zn_Superoxide_Dismutase 17 159 6.2896E-58
11 g16280.t25 Gene3D G3DSA:2.60.40.200 - 18 166 5.0E-58
2 g16280.t25 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 16 167 1.4E-60
3 g16280.t25 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 16 167 1.4E-60
7 g16280.t25 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 57 79 8.9E-41
6 g16280.t25 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 93 102 8.9E-41
5 g16280.t25 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 112 134 8.9E-41
4 g16280.t25 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 137 163 8.9E-41
1 g16280.t25 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 26 162 1.4E-47
10 g16280.t25 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 57 67 -
9 g16280.t25 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 151 162 -
8 g16280.t25 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 17 165 4.06E-53

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