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.t7 TTS g16280.t7 8956500 8956500
chr_4 g16280 g16280.t7 isoform g16280.t7 8956673 8957463
chr_4 g16280 g16280.t7 exon g16280.t7.exon1 8956673 8956897
chr_4 g16280 g16280.t7 cds g16280.t7.CDS1 8956673 8956897
chr_4 g16280 g16280.t7 exon g16280.t7.exon2 8956961 8957070
chr_4 g16280 g16280.t7 cds g16280.t7.CDS2 8956961 8957070
chr_4 g16280 g16280.t7 exon g16280.t7.exon3 8957152 8957203
chr_4 g16280 g16280.t7 cds g16280.t7.CDS3 8957152 8957203
chr_4 g16280 g16280.t7 exon g16280.t7.exon4 8957356 8957463
chr_4 g16280 g16280.t7 cds g16280.t7.CDS4 8957356 8957463
chr_4 g16280 g16280.t7 TSS g16280.t7 8957532 8957532

Sequences

>g16280.t7 Gene=g16280 Length=495
ATGGATAAGTTAAAAAAAGCATTAGATATTGAAAAAGATCATCCAGTTACAAGAGCTGTT
TGTGTCATGATTGGTGAAGCTGAAGGAACTTGCTACTTTGAACAAGCTGGTCCCGTTCAT
ATCACTGGTGAAATCAAAGGTTTAAAACCTGGCTTGCATGGTTTTCATATCCATGAATAT
GGTGACATTACCAACGGATGTATGTCTGCCGGACAGCATTTCAATCCATACAACAAACAA
CATGGAGGAACTCTTGATGACAATCGTCATGTTGGTGATTTGGGAAATATTAAAGCTGAA
GAAAATGGAATTGCAAAAATTGACATAACAGATCGAATGATTTCTCTGCATGGAAACTCG
AATATTATTGGTCGCACGTTGGTTGTACATGTAAATGCCGACGATTTGGGACTTGGGTCC
AATGAACAATCAAAATCCGACGGTAACTCTGGTGGAAGAATTAGCTGTGGTGTTATTGGC
ATCTGCAAGGCATAA

>g16280.t7 Gene=g16280 Length=164
MDKLKKALDIEKDHPVTRAVCVMIGEAEGTCYFEQAGPVHITGEIKGLKPGLHGFHIHEY
GDITNGCMSAGQHFNPYNKQHGGTLDDNRHVGDLGNIKAEENGIAKIDITDRMISLHGNS
NIIGRTLVVHVNADDLGLGSNEQSKSDGNSGGRISCGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16280.t7 CDD cd00305 Cu-Zn_Superoxide_Dismutase 17 156 1.50333E-57
11 g16280.t7 Gene3D G3DSA:2.60.40.200 - 18 163 6.9E-57
2 g16280.t7 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 16 164 4.8E-59
3 g16280.t7 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 16 164 4.8E-59
5 g16280.t7 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 54 76 8.3E-41
6 g16280.t7 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 90 99 8.3E-41
7 g16280.t7 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 109 131 8.3E-41
4 g16280.t7 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 134 160 8.3E-41
1 g16280.t7 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 26 159 2.0E-46
10 g16280.t7 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 54 64 -
9 g16280.t7 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 148 159 -
8 g16280.t7 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 18 162 5.24E-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.

Raw TPM values