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.t4 isoform g16289.t4 8979639 8980639
chr_4 g16289 g16289.t4 exon g16289.t4.exon1 8979639 8979792
chr_4 g16289 g16289.t4 TTS g16289.t4 8979680 8979680
chr_4 g16289 g16289.t4 cds g16289.t4.CDS1 8979767 8979792
chr_4 g16289 g16289.t4 exon g16289.t4.exon2 8979925 8980063
chr_4 g16289 g16289.t4 cds g16289.t4.CDS2 8979925 8980063
chr_4 g16289 g16289.t4 exon g16289.t4.exon3 8980123 8980232
chr_4 g16289 g16289.t4 cds g16289.t4.CDS3 8980123 8980232
chr_4 g16289 g16289.t4 exon g16289.t4.exon4 8980396 8980456
chr_4 g16289 g16289.t4 cds g16289.t4.CDS4 8980396 8980456
chr_4 g16289 g16289.t4 exon g16289.t4.exon5 8980577 8980639
chr_4 g16289 g16289.t4 cds g16289.t4.CDS5 8980577 8980639
chr_4 g16289 g16289.t4 TSS g16289.t4 8980729 8980729

Sequences

>g16289.t4 Gene=g16289 Length=527
ATGGTAAAAGCAGTTTGTGTAATGATAGGTGATGTCGAAGGAACATGTTTCTTTGAGCAA
GTTGATGGAAAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTA
CATGGTTTTCACGTCCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGGTCAA
CATTTCAATCCAACTAATAAAGATCATGGTGCACCGAATGTAGAAAATCGTCATGTTGGT
GATTTGGGAAATGTCGAAGCTGGAGCTGATGGAACCGCTAAAATTGACATAACTGATAAA
GTGATGTCTTTAAATGGAGAATTTAGTATTATTGGTCGAACAATGGTTGTCCACACTAAT
CCAGATGATTTGGAAGATTTTTTGAGTCTCAATCAATAGAAAATTTTTAGATTAAACTTT
TTATTACAAAGTATTATTCAAAATTTATCCAACGTAAAGTTAATAAAGTGCATGCTCTGA
AATATTAAAAAAAAGATTTTAAAAATTTAAGATGTAATCATTTAGAA

>g16289.t4 Gene=g16289 Length=132
MVKAVCVMIGDVEGTCFFEQVDGKGPVHITGEVKGLKPGLHGFHVHEYGDNTNGCMSAGQ
HFNPTNKDHGAPNVENRHVGDLGNVEAGADGTAKIDITDKVMSLNGEFSIIGRTMVVHTN
PDDLEDFLSLNQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g16289.t4 CDD cd00305 Cu-Zn_Superoxide_Dismutase 2 124 8.95037E-53
9 g16289.t4 Gene3D G3DSA:2.60.40.200 - 1 130 2.0E-49
2 g16289.t4 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 2 124 2.4E-50
3 g16289.t4 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 2 124 2.4E-50
5 g16289.t4 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 42 64 2.7E-26
6 g16289.t4 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 78 87 2.7E-26
4 g16289.t4 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 97 119 2.7E-26
1 g16289.t4 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 10 124 6.4E-42
8 g16289.t4 ProSitePatterns PS00087 Copper/Zinc superoxide dismutase signature 1. 42 52 -
7 g16289.t4 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 4 124 6.02E-46

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