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.t13 TTS g16280.t13 8956500 8956500
chr_4 g16280 g16280.t13 isoform g16280.t13 8956673 8957463
chr_4 g16280 g16280.t13 exon g16280.t13.exon1 8956673 8956897
chr_4 g16280 g16280.t13 cds g16280.t13.CDS1 8956673 8956897
chr_4 g16280 g16280.t13 exon g16280.t13.exon2 8956961 8957070
chr_4 g16280 g16280.t13 cds g16280.t13.CDS2 8956961 8957070
chr_4 g16280 g16280.t13 exon g16280.t13.exon3 8957148 8957212
chr_4 g16280 g16280.t13 cds g16280.t13.CDS3 8957148 8957154
chr_4 g16280 g16280.t13 exon g16280.t13.exon4 8957356 8957463
chr_4 g16280 g16280.t13 TSS g16280.t13 8957532 8957532

Sequences

>g16280.t13 Gene=g16280 Length=508
ATGGATAAGTTAAAAAAAGCATTAGATATTGAAAAAGATCATCCAGTTACAAGAGCTGTT
TGTGTCATGATTGGTGAAGCTGAAGGAACTTGCTACTTTGAACAAGCTTCAAAGAAGGGT
CCCGTTCATATCACTGGTGAAATCAAAGGTTTAAAACCTGGCTTGCATGGTATGTTTTCA
TATCCATGAATATGGTGACATTACCAACGGATGTATGTCTGCCGGACAGCATTTCAATCC
ATACAACAAACAACATGGAGGAACTCTTGATGACAATCGTCATGTTGGTGATTTGGGAAA
TATTAAAGCTGAAGAAAATGGAATTGCAAAAATTGACATAACAGATCGAATGATTTCTCT
GCATGGAAACTCGAATATTATTGGTCGCACGTTGGTTGTACATGTAAATGCCGACGATTT
GGGACTTGGGTCCAATGAACAATCAAAATCCGACGGTAACTCTGGTGGAAGAATTAGCTG
TGGTGTTATTGGCATCTGCAAGGCATAA

>g16280.t13 Gene=g16280 Length=113
MVCFHIHEYGDITNGCMSAGQHFNPYNKQHGGTLDDNRHVGDLGNIKAEENGIAKIDITD
RMISLHGNSNIIGRTLVVHVNADDLGLGSNEQSKSDGNSGGRISCGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16280.t13 CDD cd00305 Cu-Zn_Superoxide_Dismutase 4 105 1.6484E-43
10 g16280.t13 Gene3D G3DSA:2.60.40.200 - 2 112 1.4E-44
2 g16280.t13 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 4 113 1.7E-46
3 g16280.t13 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 4 113 1.7E-46
7 g16280.t13 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 3 25 5.4E-40
5 g16280.t13 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 39 48 5.4E-40
6 g16280.t13 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 58 80 5.4E-40
4 g16280.t13 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 83 109 5.4E-40
1 g16280.t13 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 4 108 5.7E-37
9 g16280.t13 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 97 108 -
8 g16280.t13 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 4 111 3.27E-42

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