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.t5 TTS g16280.t5 8956500 8956500
chr_4 g16280 g16280.t5 isoform g16280.t5 8956673 8957068
chr_4 g16280 g16280.t5 exon g16280.t5.exon1 8956673 8956897
chr_4 g16280 g16280.t5 cds g16280.t5.CDS1 8956673 8956897
chr_4 g16280 g16280.t5 exon g16280.t5.exon2 8956961 8957068
chr_4 g16280 g16280.t5 cds g16280.t5.CDS2 8956961 8957029
chr_4 g16280 g16280.t5 TSS g16280.t5 8957532 8957532

Sequences

>g16280.t5 Gene=g16280 Length=333
TTTCATATCCATGAATATGGTGACATTACCAACGGATGTATGTCTGCCGGACAGCATTTC
AATCCATACAACAAACAACATGGAGGAACTCTTGATGACAATCGTCATGTTGGTGATTTG
GGAAATATTAAAGCTGAAGAAAATGGAATTGCAAAAATTGACATAACAGATCGAATGATT
TCTCTGCATGGAAACTCGAATATTATTGGTCGCACGTTGGTTGTACATGTAAATGCCGAC
GATTTGGGACTTGGGTCCAATGAACAATCAAAATCCGACGGTAACTCTGGTGGAAGAATT
AGCTGTGGTGTTATTGGCATCTGCAAGGCATAA

>g16280.t5 Gene=g16280 Length=97
MSAGQHFNPYNKQHGGTLDDNRHVGDLGNIKAEENGIAKIDITDRMISLHGNSNIIGRTL
VVHVNADDLGLGSNEQSKSDGNSGGRISCGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g16280.t5 CDD cd00305 Cu-Zn_Superoxide_Dismutase 1 89 1.40044E-33
8 g16280.t5 Gene3D G3DSA:2.60.40.200 - 1 96 4.5E-36
11 g16280.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
12 g16280.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 15 -
2 g16280.t5 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 2 97 9.9E-38
3 g16280.t5 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 2 97 9.9E-38
6 g16280.t5 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 23 32 1.6E-26
4 g16280.t5 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 42 64 1.6E-26
5 g16280.t5 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 67 93 1.6E-26
1 g16280.t5 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 2 92 2.7E-29
10 g16280.t5 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 81 92 -
7 g16280.t5 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 1 95 5.89E-34

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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