Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t15 TTS g16289.t15 8979680 8979680
chr_4 g16289 g16289.t15 isoform g16289.t15 8979839 8980639
chr_4 g16289 g16289.t15 exon g16289.t15.exon1 8979839 8980063
chr_4 g16289 g16289.t15 cds g16289.t15.CDS1 8979839 8980063
chr_4 g16289 g16289.t15 exon g16289.t15.exon2 8980123 8980232
chr_4 g16289 g16289.t15 cds g16289.t15.CDS2 8980123 8980232
chr_4 g16289 g16289.t15 exon g16289.t15.exon3 8980396 8980456
chr_4 g16289 g16289.t15 cds g16289.t15.CDS3 8980396 8980456
chr_4 g16289 g16289.t15 exon g16289.t15.exon4 8980580 8980639
chr_4 g16289 g16289.t15 cds g16289.t15.CDS4 8980580 8980639
chr_4 g16289 g16289.t15 TSS g16289.t15 8980729 8980729

Sequences

>g16289.t15 Gene=g16289 Length=456
ATGGTAAAAGCAGTTTGTGTAATGATAGGTGATGTCGAAGGAACATGTTTCTTTGAGCAA
GATGGAAAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTACAT
GGTTTTCACGTCCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGGTCAACAT
TTCAATCCAACTAATAAAGATCATGGTGCACCGAATGTAGAAAATCGTCATGTTGGTGAT
TTGGGAAATGTCGAAGCTGGAGCTGATGGAACCGCTAAAATTGACATAACTGATAAAGTG
ATGTCTTTAAATGGAGAATTTAGTATTATTGGTCGAACAATGGTTGTCCACACTAATCCA
GATGATTTGGGTGTTGGTGGTGCAGAAACATCAAAGAAAGACGGTAACGCTGGTGGCCGC
CTGGCTTGCGGCGTTATTGGCATCTGCAAGGCATAA

>g16289.t15 Gene=g16289 Length=151
MVKAVCVMIGDVEGTCFFEQDGKGPVHITGEVKGLKPGLHGFHVHEYGDNTNGCMSAGQH
FNPTNKDHGAPNVENRHVGDLGNVEAGADGTAKIDITDKVMSLNGEFSIIGRTMVVHTNP
DDLGVGGAETSKKDGNAGGRLACGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16289.t15 CDD cd00305 Cu-Zn_Superoxide_Dismutase 2 143 1.16716E-60
11 g16289.t15 Gene3D G3DSA:2.60.40.200 - 3 150 1.1E-60
2 g16289.t15 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 2 151 2.0E-65
3 g16289.t15 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 2 151 2.0E-65
6 g16289.t15 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 41 63 2.5E-42
4 g16289.t15 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 77 86 2.5E-42
5 g16289.t15 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 96 118 2.5E-42
7 g16289.t15 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 121 147 2.5E-42
1 g16289.t15 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 10 146 3.0E-49
10 g16289.t15 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 41 51 -
9 g16289.t15 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 135 146 -
8 g16289.t15 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 4 149 5.37E-55

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

Pathway

  • This transcript belongs to the following pathways

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