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.t18 TTS g16289.t18 8979680 8979680
chr_4 g16289 g16289.t18 isoform g16289.t18 8979839 8980639
chr_4 g16289 g16289.t18 exon g16289.t18.exon1 8979839 8980063
chr_4 g16289 g16289.t18 cds g16289.t18.CDS1 8979839 8980063
chr_4 g16289 g16289.t18 exon g16289.t18.exon2 8980123 8980221
chr_4 g16289 g16289.t18 cds g16289.t18.CDS2 8980123 8980221
chr_4 g16289 g16289.t18 exon g16289.t18.exon3 8980396 8980456
chr_4 g16289 g16289.t18 cds g16289.t18.CDS3 8980396 8980456
chr_4 g16289 g16289.t18 exon g16289.t18.exon4 8980577 8980639
chr_4 g16289 g16289.t18 cds g16289.t18.CDS4 8980577 8980608
chr_4 g16289 g16289.t18 TSS g16289.t18 8980729 8980729

Sequences

>g16289.t18 Gene=g16289 Length=448
ATGGTAAAAGCAGTTTGTGTAATGATAGGTGATGTCGAAGGAACATGTTTCTTTGAGCAA
GTTGATGGAAAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTA
CATGCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGGTCAACATTTCAATCC
AACTAATAAAGATCATGGTGCACCGAATGTAGAAAATCGTCATGTTGGTGATTTGGGAAA
TGTCGAAGCTGGAGCTGATGGAACCGCTAAAATTGACATAACTGATAAAGTGATGTCTTT
AAATGGAGAATTTAGTATTATTGGTCGAACAATGGTTGTCCACACTAATCCAGATGATTT
GGGTGTTGGTGGTGCAGAAACATCAAAGAAAGACGGTAACGCTGGTGGCCGCCTGGCTTG
CGGCGTTATTGGCATCTGCAAGGCATAA

>g16289.t18 Gene=g16289 Length=138
MSKEHVSLSKLMEKAQFILPVRSKVLNLDYMHEYGDNTNGCMSAGQHFNPTNKDHGAPNV
ENRHVGDLGNVEAGADGTAKIDITDKVMSLNGEFSIIGRTMVVHTNPDDLGVGGAETSKK
DGNAGGRLACGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16289.t18 CDD cd00305 Cu-Zn_Superoxide_Dismutase 32 130 2.28267E-47
10 g16289.t18 Gene3D G3DSA:2.60.40.200 - 30 136 2.8E-44
2 g16289.t18 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 31 138 1.1E-48
3 g16289.t18 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 31 138 1.1E-48
5 g16289.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 28 50 1.5E-38
7 g16289.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 64 73 1.5E-38
6 g16289.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 83 105 1.5E-38
4 g16289.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 108 134 1.5E-38
1 g16289.t18 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 32 133 4.0E-36
9 g16289.t18 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 122 133 -
8 g16289.t18 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 31 136 5.1E-42

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