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 g16289 g16289.t6 TTS g16289.t6 8979680 8979680
chr_4 g16289 g16289.t6 isoform g16289.t6 8979839 8980450
chr_4 g16289 g16289.t6 exon g16289.t6.exon1 8979839 8980063
chr_4 g16289 g16289.t6 cds g16289.t6.CDS1 8979839 8980063
chr_4 g16289 g16289.t6 exon g16289.t6.exon2 8980123 8980227
chr_4 g16289 g16289.t6 cds g16289.t6.CDS2 8980123 8980227
chr_4 g16289 g16289.t6 exon g16289.t6.exon3 8980396 8980450
chr_4 g16289 g16289.t6 cds g16289.t6.CDS3 8980396 8980398
chr_4 g16289 g16289.t6 TSS g16289.t6 8980729 8980729

Sequences

>g16289.t6 Gene=g16289 Length=385
AAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTACATGCACGT
CCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGGTCAACATTTCAATCCAAC
TAATAAAGATCATGGTGCACCGAATGTAGAAAATCGTCATGTTGGTGATTTGGGAAATGT
CGAAGCTGGAGCTGATGGAACCGCTAAAATTGACATAACTGATAAAGTGATGTCTTTAAA
TGGAGAATTTAGTATTATTGGTCGAACAATGGTTGTCCACACTAATCCAGATGATTTGGG
TGTTGGTGGTGCAGAAACATCAAAGAAAGACGGTAACGCTGGTGGCCGCCTGGCTTGCGG
CGTTATTGGCATCTGCAAGGCATAA

>g16289.t6 Gene=g16289 Length=110
MHVHEYGDNTNGCMSAGQHFNPTNKDHGAPNVENRHVGDLGNVEAGADGTAKIDITDKVM
SLNGEFSIIGRTMVVHTNPDDLGVGGAETSKKDGNAGGRLACGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g16289.t6 CDD cd00305 Cu-Zn_Superoxide_Dismutase 1 102 8.85471E-46
9 g16289.t6 Gene3D G3DSA:2.60.40.200 - 1 110 1.5E-46
2 g16289.t6 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 1 110 4.4E-50
3 g16289.t6 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 1 110 4.4E-50
5 g16289.t6 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 36 45 3.0E-27
4 g16289.t6 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 55 77 3.0E-27
6 g16289.t6 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 80 106 3.0E-27
1 g16289.t6 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 1 105 1.4E-38
8 g16289.t6 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 94 105 -
7 g16289.t6 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 1 108 1.44E-43

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