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_2 g8507 g8507.t4 isoform g8507.t4 31066653 31067483
chr_2 g8507 g8507.t4 exon g8507.t4.exon1 31066653 31066864
chr_2 g8507 g8507.t4 TTS g8507.t4 31066661 31066661
chr_2 g8507 g8507.t4 cds g8507.t4.CDS1 31066833 31066864
chr_2 g8507 g8507.t4 exon g8507.t4.exon2 31066927 31067119
chr_2 g8507 g8507.t4 cds g8507.t4.CDS2 31066927 31067119
chr_2 g8507 g8507.t4 exon g8507.t4.exon3 31067181 31067218
chr_2 g8507 g8507.t4 cds g8507.t4.CDS3 31067181 31067218
chr_2 g8507 g8507.t4 exon g8507.t4.exon4 31067284 31067355
chr_2 g8507 g8507.t4 cds g8507.t4.CDS4 31067284 31067314
chr_2 g8507 g8507.t4 exon g8507.t4.exon5 31067423 31067483
chr_2 g8507 g8507.t4 TSS g8507.t4 31067822 31067822

Sequences

>g8507.t4 Gene=g8507 Length=576
TCTGATAAAGATGAAGTTCATGTCACAGGAGAAGTTAAAGGCCTAAAAGCTGGTTTGCAC
GGCTTCCATATTCATGAATTCGGAGACAATACAAATGGCTGCATGTCTGCTGGTGCTCAT
TTTAATCCTTTTGGAAAAGACCATGCCGCTCCGACTGATGCTGATCGTCATGTTGGAGAT
TTAGGAAATATCACTGCCGGAGATGATGGTGTTGCTAAGGTTGACATCACTGATAAAATG
ATTTCATTGAGTGGTGAATTGAATATCATAGGAAGAACAGTTGTTGTTCACGCTGATCCT
GATGACCTCGGACGTGGTGGACATGATTTGTCAAAGACCACAGGAAATGCTGGTGGCAGA
TTAGCTTGTGGCGTTATTGGCATTTGTAAGGAATAAACATTTAAATATATATCATGAATT
TCAAAAAATACCTACTACAGGCTCTTCTCATACACCAAATTCCTTTTCTAATGTCACTGC
AAGACTTTAAAAAAATTACTTTTTGTCTGTAGAAAAATTATATCCTAAGGTGGAAGTAAA
TAAAATTTTCATTATCATTGATTGGTACAATTCAAA

>g8507.t4 Gene=g8507 Length=97
MSAGAHFNPFGKDHAAPTDADRHVGDLGNITAGDDGVAKVDITDKMISLSGELNIIGRTV
VVHADPDDLGRGGHDLSKTTGNAGGRLACGVIGICKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g8507.t4 CDD cd00305 Cu-Zn_Superoxide_Dismutase 1 89 5.58978E-39
8 g8507.t4 Gene3D G3DSA:2.60.40.200 - 1 97 3.8E-40
11 g8507.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
2 g8507.t4 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 2 96 2.3E-42
3 g8507.t4 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 2 96 2.3E-42
6 g8507.t4 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 23 32 1.9E-28
4 g8507.t4 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 42 64 1.9E-28
5 g8507.t4 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 67 93 1.9E-28
1 g8507.t4 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 2 92 2.0E-31
10 g8507.t4 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 81 92 -
7 g8507.t4 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 1 95 4.97E-38

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