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.t1 TTS g16289.t1 8979680 8979680
chr_4 g16289 g16289.t1 isoform g16289.t1 8979839 8980639
chr_4 g16289 g16289.t1 exon g16289.t1.exon1 8979839 8980063
chr_4 g16289 g16289.t1 cds g16289.t1.CDS1 8979839 8980063
chr_4 g16289 g16289.t1 exon g16289.t1.exon2 8980123 8980232
chr_4 g16289 g16289.t1 cds g16289.t1.CDS2 8980123 8980232
chr_4 g16289 g16289.t1 exon g16289.t1.exon3 8980396 8980456
chr_4 g16289 g16289.t1 cds g16289.t1.CDS3 8980396 8980456
chr_4 g16289 g16289.t1 exon g16289.t1.exon4 8980577 8980639
chr_4 g16289 g16289.t1 cds g16289.t1.CDS4 8980577 8980639
chr_4 g16289 g16289.t1 TSS g16289.t1 8980729 8980729

Sequences

>g16289.t1 Gene=g16289 Length=459
ATGGTAAAAGCAGTTTGTGTAATGATAGGTGATGTCGAAGGAACATGTTTCTTTGAGCAA
GTTGATGGAAAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTA
CATGGTTTTCACGTCCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGGTCAA
CATTTCAATCCAACTAATAAAGATCATGGTGCACCGAATGTAGAAAATCGTCATGTTGGT
GATTTGGGAAATGTCGAAGCTGGAGCTGATGGAACCGCTAAAATTGACATAACTGATAAA
GTGATGTCTTTAAATGGAGAATTTAGTATTATTGGTCGAACAATGGTTGTCCACACTAAT
CCAGATGATTTGGGTGTTGGTGGTGCAGAAACATCAAAGAAAGACGGTAACGCTGGTGGC
CGCCTGGCTTGCGGCGTTATTGGCATCTGCAAGGCATAA

>g16289.t1 Gene=g16289 Length=152
MVKAVCVMIGDVEGTCFFEQVDGKGPVHITGEVKGLKPGLHGFHVHEYGDNTNGCMSAGQ
HFNPTNKDHGAPNVENRHVGDLGNVEAGADGTAKIDITDKVMSLNGEFSIIGRTMVVHTN
PDDLGVGGAETSKKDGNAGGRLACGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16289.t1 CDD cd00305 Cu-Zn_Superoxide_Dismutase 2 144 2.07431E-60
11 g16289.t1 Gene3D G3DSA:2.60.40.200 - 3 151 1.0E-59
2 g16289.t1 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 2 152 3.6E-64
3 g16289.t1 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 2 152 3.6E-64
5 g16289.t1 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 42 64 2.5E-42
7 g16289.t1 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 78 87 2.5E-42
4 g16289.t1 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 97 119 2.5E-42
6 g16289.t1 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 122 148 2.5E-42
1 g16289.t1 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 10 147 3.8E-49
10 g16289.t1 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 42 52 -
9 g16289.t1 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 136 147 -
8 g16289.t1 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 4 150 1.01E-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.

Raw TPM values