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.t15 TTS g16280.t15 8956500 8956500
chr_4 g16280 g16280.t15 isoform g16280.t15 8956673 8957463
chr_4 g16280 g16280.t15 exon g16280.t15.exon1 8956673 8956897
chr_4 g16280 g16280.t15 cds g16280.t15.CDS1 8956673 8956897
chr_4 g16280 g16280.t15 exon g16280.t15.exon2 8956966 8957070
chr_4 g16280 g16280.t15 cds g16280.t15.CDS2 8956966 8957052
chr_4 g16280 g16280.t15 exon g16280.t15.exon3 8957152 8957212
chr_4 g16280 g16280.t15 exon g16280.t15.exon4 8957356 8957463
chr_4 g16280 g16280.t15 TSS g16280.t15 8957532 8957532

Sequences

>g16280.t15 Gene=g16280 Length=499
ATGGATAAGTTAAAAAAAGCATTAGATATTGAAAAAGATCATCCAGTTACAAGAGCTGTT
TGTGTCATGATTGGTGAAGCTGAAGGAACTTGCTACTTTGAACAAGCTTCAAAGAAGGGT
CCCGTTCATATCACTGGTGAAATCAAAGGTTTAAAACCTGGCTTGCATGGTTTTCATATC
CATGAATATGGTGACATTACCAACGGATGTATGTCTGCCGGACAGCATTTCAATCCATAC
AACAAACAACATGGAGGAACTCTTGATGACAATCGTTGGTGATTTGGGAAATATTAAAGC
TGAAGAAAATGGAATTGCAAAAATTGACATAACAGATCGAATGATTTCTCTGCATGGAAA
CTCGAATATTATTGGTCGCACGTTGGTTGTACATGTAAATGCCGACGATTTGGGACTTGG
GTCCAATGAACAATCAAAATCCGACGGTAACTCTGGTGGAAGAATTAGCTGTGGTGTTAT
TGGCATCTGCAAGGCATAA

>g16280.t15 Gene=g16280 Length=103
MVTLPTDVCLPDSISIHTTNNMEELLMTIVGDLGNIKAEENGIAKIDITDRMISLHGNSN
IIGRTLVVHVNADDLGLGSNEQSKSDGNSGGRISCGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g16280.t15 Gene3D G3DSA:2.60.40.200 - 14 103 6.8E-26
2 g16280.t15 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 29 103 6.2E-25
3 g16280.t15 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 29 103 6.2E-25
6 g16280.t15 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 29 38 1.2E-24
4 g16280.t15 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 48 70 1.2E-24
5 g16280.t15 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 73 99 1.2E-24
1 g16280.t15 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 27 98 7.6E-20
8 g16280.t15 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 87 98 -
7 g16280.t15 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 28 100 3.01E-23

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. There were no conditions that were differentially expressed