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.t11 TTS g16289.t11 8979680 8979680
chr_4 g16289 g16289.t11 isoform g16289.t11 8979839 8980639
chr_4 g16289 g16289.t11 exon g16289.t11.exon1 8979839 8980063
chr_4 g16289 g16289.t11 cds g16289.t11.CDS1 8979839 8980063
chr_4 g16289 g16289.t11 exon g16289.t11.exon2 8980123 8980227
chr_4 g16289 g16289.t11 cds g16289.t11.CDS2 8980123 8980227
chr_4 g16289 g16289.t11 exon g16289.t11.exon3 8980396 8980456
chr_4 g16289 g16289.t11 cds g16289.t11.CDS3 8980396 8980456
chr_4 g16289 g16289.t11 exon g16289.t11.exon4 8980577 8980639
chr_4 g16289 g16289.t11 cds g16289.t11.CDS4 8980577 8980608
chr_4 g16289 g16289.t11 TSS g16289.t11 8980729 8980729

Sequences

>g16289.t11 Gene=g16289 Length=454
ATGGTAAAAGCAGTTTGTGTAATGATAGGTGATGTCGAAGGAACATGTTTCTTTGAGCAA
GTTGATGGAAAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTA
CATGCACGTCCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGGTCAACATTT
CAATCCAACTAATAAAGATCATGGTGCACCGAATGTAGAAAATCGTCATGTTGGTGATTT
GGGAAATGTCGAAGCTGGAGCTGATGGAACCGCTAAAATTGACATAACTGATAAAGTGAT
GTCTTTAAATGGAGAATTTAGTATTATTGGTCGAACAATGGTTGTCCACACTAATCCAGA
TGATTTGGGTGTTGGTGGTGCAGAAACATCAAAGAAAGACGGTAACGCTGGTGGCCGCCT
GGCTTGCGGCGTTATTGGCATCTGCAAGGCATAA

>g16289.t11 Gene=g16289 Length=140
MSKEHVSLSKLMEKAQFILPVRSKVLNLDYMHVHEYGDNTNGCMSAGQHFNPTNKDHGAP
NVENRHVGDLGNVEAGADGTAKIDITDKVMSLNGEFSIIGRTMVVHTNPDDLGVGGAETS
KKDGNAGGRLACGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16289.t11 CDD cd00305 Cu-Zn_Superoxide_Dismutase 31 132 3.90873E-49
10 g16289.t11 Gene3D G3DSA:2.60.40.200 - 11 139 2.4E-47
2 g16289.t11 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 31 140 2.6E-50
3 g16289.t11 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 31 140 2.6E-50
7 g16289.t11 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 30 52 2.4E-40
5 g16289.t11 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 66 75 2.4E-40
4 g16289.t11 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 85 107 2.4E-40
6 g16289.t11 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 110 136 2.4E-40
1 g16289.t11 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 31 135 2.2E-39
9 g16289.t11 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 124 135 -
8 g16289.t11 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 29 138 1.7E-44

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. There were no conditions that were differentially expressed