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.t17 TTS g16280.t17 8956500 8956500
chr_4 g16280 g16280.t17 isoform g16280.t17 8956673 8957463
chr_4 g16280 g16280.t17 exon g16280.t17.exon1 8956673 8956713
chr_4 g16280 g16280.t17 cds g16280.t17.CDS1 8956673 8956713
chr_4 g16280 g16280.t17 exon g16280.t17.exon2 8956768 8956897
chr_4 g16280 g16280.t17 cds g16280.t17.CDS2 8956768 8956897
chr_4 g16280 g16280.t17 exon g16280.t17.exon3 8956961 8957070
chr_4 g16280 g16280.t17 cds g16280.t17.CDS3 8956961 8957070
chr_4 g16280 g16280.t17 exon g16280.t17.exon4 8957152 8957206
chr_4 g16280 g16280.t17 cds g16280.t17.CDS4 8957152 8957206
chr_4 g16280 g16280.t17 exon g16280.t17.exon5 8957356 8957463
chr_4 g16280 g16280.t17 cds g16280.t17.CDS5 8957356 8957463
chr_4 g16280 g16280.t17 TSS g16280.t17 8957532 8957532

Sequences

>g16280.t17 Gene=g16280 Length=444
ATGGATAAGTTAAAAAAAGCATTAGATATTGAAAAAGATCATCCAGTTACAAGAGCTGTT
TGTGTCATGATTGGTGAAGCTGAAGGAACTTGCTACTTTGAACAAGCTAAGGGTCCCGTT
CATATCACTGGTGAAATCAAAGGTTTAAAACCTGGCTTGCATGGTTTTCATATCCATGAA
TATGGTGACATTACCAACGGATGTATGTCTGCCGGACAGCATTTCAATCCATACAACAAA
CAACATGGAGGAACTCTTGATGACAATCGTCATGTTGGTGATTTGGGAAATATTAAAGCT
GAAGAAAATGGAATTGCAAAAATTGACATAACAGATCGAATGATTTCTCTGCATGGAAAC
TCGAATATTATTGGTCGCACGTTGGTTGTACATGTAAATGCCGGAAGAATTAGCTGTGGT
GTTATTGGCATCTGCAAGGCATAA

>g16280.t17 Gene=g16280 Length=147
MDKLKKALDIEKDHPVTRAVCVMIGEAEGTCYFEQAKGPVHITGEIKGLKPGLHGFHIHE
YGDITNGCMSAGQHFNPYNKQHGGTLDDNRHVGDLGNIKAEENGIAKIDITDRMISLHGN
SNIIGRTLVVHVNAGRISCGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g16280.t17 CDD cd00305 Cu-Zn_Superoxide_Dismutase 17 145 1.55909E-50
9 g16280.t17 Gene3D G3DSA:2.60.40.200 - 9 145 1.6E-47
2 g16280.t17 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 16 132 2.7E-45
3 g16280.t17 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 16 132 2.7E-45
4 g16280.t17 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 55 77 1.8E-25
5 g16280.t17 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 91 100 1.8E-25
6 g16280.t17 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 110 132 1.8E-25
1 g16280.t17 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 26 142 2.3E-38
8 g16280.t17 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 55 65 -
7 g16280.t17 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 19 145 1.83E-44

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