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 g16280 g16280.t18 TTS g16280.t18 8956500 8956500
chr_4 g16280 g16280.t18 isoform g16280.t18 8956673 8957463
chr_4 g16280 g16280.t18 exon g16280.t18.exon1 8956673 8956897
chr_4 g16280 g16280.t18 cds g16280.t18.CDS1 8956673 8956897
chr_4 g16280 g16280.t18 exon g16280.t18.exon2 8956961 8957070
chr_4 g16280 g16280.t18 cds g16280.t18.CDS2 8956961 8957070
chr_4 g16280 g16280.t18 exon g16280.t18.exon3 8957152 8957194
chr_4 g16280 g16280.t18 cds g16280.t18.CDS3 8957152 8957194
chr_4 g16280 g16280.t18 exon g16280.t18.exon4 8957356 8957463
chr_4 g16280 g16280.t18 cds g16280.t18.CDS4 8957356 8957463
chr_4 g16280 g16280.t18 TSS g16280.t18 8957532 8957532

Sequences

>g16280.t18 Gene=g16280 Length=486
ATGGATAAGTTAAAAAAAGCATTAGATATTGAAAAAGATCATCCAGTTACAAGAGCTGTT
TGTGTCATGATTGGTGAAGCTGAAGGAACTTGCTACTTTGAACAAGCTCATATCACTGGT
GAAATCAAAGGTTTAAAACCTGGCTTGCATGGTTTTCATATCCATGAATATGGTGACATT
ACCAACGGATGTATGTCTGCCGGACAGCATTTCAATCCATACAACAAACAACATGGAGGA
ACTCTTGATGACAATCGTCATGTTGGTGATTTGGGAAATATTAAAGCTGAAGAAAATGGA
ATTGCAAAAATTGACATAACAGATCGAATGATTTCTCTGCATGGAAACTCGAATATTATT
GGTCGCACGTTGGTTGTACATGTAAATGCCGACGATTTGGGACTTGGGTCCAATGAACAA
TCAAAATCCGACGGTAACTCTGGTGGAAGAATTAGCTGTGGTGTTATTGGCATCTGCAAG
GCATAA

>g16280.t18 Gene=g16280 Length=161
MDKLKKALDIEKDHPVTRAVCVMIGEAEGTCYFEQAHITGEIKGLKPGLHGFHIHEYGDI
TNGCMSAGQHFNPYNKQHGGTLDDNRHVGDLGNIKAEENGIAKIDITDRMISLHGNSNII
GRTLVVHVNADDLGLGSNEQSKSDGNSGGRISCGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16280.t18 CDD cd00305 Cu-Zn_Superoxide_Dismutase 17 153 5.47189E-56
11 g16280.t18 Gene3D G3DSA:2.60.40.200 - 18 160 4.2E-55
2 g16280.t18 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 16 161 1.9E-56
3 g16280.t18 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 16 161 1.9E-56
5 g16280.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 51 73 8.1E-41
7 g16280.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 87 96 8.1E-41
4 g16280.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 106 128 8.1E-41
6 g16280.t18 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 131 157 8.1E-41
1 g16280.t18 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 26 156 2.0E-44
10 g16280.t18 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 51 61 -
9 g16280.t18 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 145 156 -
8 g16280.t18 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 19 159 1.28E-49

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

Pathway

  • This transcript belongs to the following pathways

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