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.t23 TTS g16289.t23 8979680 8979680
chr_4 g16289 g16289.t23 isoform g16289.t23 8979839 8980639
chr_4 g16289 g16289.t23 exon g16289.t23.exon1 8979839 8980063
chr_4 g16289 g16289.t23 cds g16289.t23.CDS1 8979839 8980063
chr_4 g16289 g16289.t23 exon g16289.t23.exon2 8980149 8980232
chr_4 g16289 g16289.t23 cds g16289.t23.CDS2 8980149 8980232
chr_4 g16289 g16289.t23 exon g16289.t23.exon3 8980396 8980456
chr_4 g16289 g16289.t23 cds g16289.t23.CDS3 8980396 8980456
chr_4 g16289 g16289.t23 exon g16289.t23.exon4 8980577 8980639
chr_4 g16289 g16289.t23 cds g16289.t23.CDS4 8980577 8980608
chr_4 g16289 g16289.t23 TSS g16289.t23 8980729 8980729

Sequences

>g16289.t23 Gene=g16289 Length=433
ATGGTAAAAGCAGTTTGTGTAATGATAGGTGATGTCGAAGGAACATGTTTCTTTGAGCAA
GTTGATGGAAAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTA
CATGGTTTTCACGTCCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGGTCAA
CATTTCAATCCAACTAATAAAGATCATGGTTGGTGATTTGGGAAATGTCGAAGCTGGAGC
TGATGGAACCGCTAAAATTGACATAACTGATAAAGTGATGTCTTTAAATGGAGAATTTAG
TATTATTGGTCGAACAATGGTTGTCCACACTAATCCAGATGATTTGGGTGTTGGTGGTGC
AGAAACATCAAAGAAAGACGGTAACGCTGGTGGCCGCCTGGCTTGCGGCGTTATTGGCAT
CTGCAAGGCATAA

>g16289.t23 Gene=g16289 Length=133
MSKEHVSLSKLMEKAQFILPVRSKVLNLDYMVFTSMNMVTIPMAACQLVNISIQLIKIMV
GDLGNVEAGADGTAKIDITDKVMSLNGEFSIIGRTMVVHTNPDDLGVGGAETSKKDGNAG
GRLACGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g16289.t23 Gene3D G3DSA:2.60.40.200 - 47 133 5.9E-27
2 g16289.t23 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 59 133 9.5E-28
3 g16289.t23 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 59 133 9.5E-28
6 g16289.t23 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 59 68 1.8E-25
5 g16289.t23 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 78 100 1.8E-25
4 g16289.t23 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 103 129 1.8E-25
1 g16289.t23 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 59 128 8.8E-21
11 g16289.t23 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 29 -
12 g16289.t23 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 30 49 -
10 g16289.t23 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 50 133 -
8 g16289.t23 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 117 128 -
7 g16289.t23 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 59 131 1.7E-24

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