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_2 g8507 g8507.t12 TTS g8507.t12 31066661 31066661
chr_2 g8507 g8507.t12 isoform g8507.t12 31066739 31067728
chr_2 g8507 g8507.t12 exon g8507.t12.exon1 31066739 31066788
chr_2 g8507 g8507.t12 cds g8507.t12.CDS1 31066739 31066788
chr_2 g8507 g8507.t12 exon g8507.t12.exon2 31066927 31067119
chr_2 g8507 g8507.t12 cds g8507.t12.CDS2 31066927 31067119
chr_2 g8507 g8507.t12 exon g8507.t12.exon3 31067181 31067218
chr_2 g8507 g8507.t12 cds g8507.t12.CDS3 31067181 31067218
chr_2 g8507 g8507.t12 exon g8507.t12.exon4 31067284 31067355
chr_2 g8507 g8507.t12 cds g8507.t12.CDS4 31067284 31067355
chr_2 g8507 g8507.t12 exon g8507.t12.exon5 31067423 31067483
chr_2 g8507 g8507.t12 cds g8507.t12.CDS5 31067423 31067483
chr_2 g8507 g8507.t12 exon g8507.t12.exon6 31067666 31067728
chr_2 g8507 g8507.t12 cds g8507.t12.CDS6 31067666 31067728
chr_2 g8507 g8507.t12 TSS g8507.t12 31067822 31067822

Sequences

>g8507.t12 Gene=g8507 Length=477
ATGCCAAAAGCCGTATGCGTACTAAAAGGAGAAGTTGAAGGAACTGTCTTCTTTCAACAA
GCTTCTGATAAAGATGAAGTTCATGTCACAGGAGAAGTTAAAGGCCTAAAAGCTGGTTTG
CACGGCTTCCATATTCATGAATTCGGAGACAATACAAATGGCTGCATGTCTGCTGGTGCT
CATTTTAATCCTTTTGGAAAAGACCATGCCGCTCCGACTGATGCTGATCGTCATGTTGGA
GATTTAGGAAATATCACTGCCGGAGATGATGGTGTTGCTAAGGTTGACATCACTGATAAA
ATGATTTCATTGAGTGGTGAATTGAATATCATAGGAAGAACAGTTGTTGTTCACGCTGAT
CCTGATGACCTCGGACGTGGTGGACATGATTTGTCAAAGACCACAGGAAATGCTGGTGGC
AGATTAGGCTCTTCTCATACACCAAATTCCTTTTCTAATGTCACTGCAAGACTTTAA

>g8507.t12 Gene=g8507 Length=158
MPKAVCVLKGEVEGTVFFQQASDKDEVHVTGEVKGLKAGLHGFHIHEFGDNTNGCMSAGA
HFNPFGKDHAAPTDADRHVGDLGNITAGDDGVAKVDITDKMISLSGELNIIGRTVVVHAD
PDDLGRGGHDLSKTTGNAGGRLGSSHTPNSFSNVTARL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g8507.t12 CDD cd00305 Cu-Zn_Superoxide_Dismutase 2 143 9.90284E-62
9 g8507.t12 Gene3D G3DSA:2.60.40.200 - 1 146 3.6E-57
13 g8507.t12 MobiDBLite mobidb-lite consensus disorder prediction 135 158 -
12 g8507.t12 MobiDBLite mobidb-lite consensus disorder prediction 137 158 -
2 g8507.t12 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 3 143 3.8E-61
3 g8507.t12 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 3 143 3.8E-61
5 g8507.t12 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 42 64 6.6E-40
7 g8507.t12 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 78 87 6.6E-40
4 g8507.t12 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 97 119 6.6E-40
6 g8507.t12 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 122 148 6.6E-40
1 g8507.t12 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 10 142 5.8E-46
11 g8507.t12 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 42 52 -
8 g8507.t12 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 4 143 8.38E-53

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