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.t9 TTS g16289.t9 8979680 8979680
chr_4 g16289 g16289.t9 isoform g16289.t9 8979839 8980639
chr_4 g16289 g16289.t9 exon g16289.t9.exon1 8979839 8980063
chr_4 g16289 g16289.t9 cds g16289.t9.CDS1 8979839 8980063
chr_4 g16289 g16289.t9 exon g16289.t9.exon2 8980123 8980232
chr_4 g16289 g16289.t9 cds g16289.t9.CDS2 8980123 8980232
chr_4 g16289 g16289.t9 exon g16289.t9.exon3 8980392 8980456
chr_4 g16289 g16289.t9 cds g16289.t9.CDS3 8980392 8980456
chr_4 g16289 g16289.t9 exon g16289.t9.exon4 8980577 8980639
chr_4 g16289 g16289.t9 cds g16289.t9.CDS4 8980577 8980608
chr_4 g16289 g16289.t9 TSS g16289.t9 8980729 8980729

Sequences

>g16289.t9 Gene=g16289 Length=463
ATGGTAAAAGCAGTTTGTGTAATGATAGGTGATGTCGAAGGAACATGTTTCTTTGAGCAA
GTTGATGGAAAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTA
CATGGTGAGTTTTCACGTCCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGG
TCAACATTTCAATCCAACTAATAAAGATCATGGTGCACCGAATGTAGAAAATCGTCATGT
TGGTGATTTGGGAAATGTCGAAGCTGGAGCTGATGGAACCGCTAAAATTGACATAACTGA
TAAAGTGATGTCTTTAAATGGAGAATTTAGTATTATTGGTCGAACAATGGTTGTCCACAC
TAATCCAGATGATTTGGGTGTTGGTGGTGCAGAAACATCAAAGAAAGACGGTAACGCTGG
TGGCCGCCTGGCTTGCGGCGTTATTGGCATCTGCAAGGCATAA

>g16289.t9 Gene=g16289 Length=143
MSKEHVSLSKLMEKAQFILPVRSKVLNLDYMVSFHVHEYGDNTNGCMSAGQHFNPTNKDH
GAPNVENRHVGDLGNVEAGADGTAKIDITDKVMSLNGEFSIIGRTMVVHTNPDDLGVGGA
ETSKKDGNAGGRLACGVIGICKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16289.t9 CDD cd00305 Cu-Zn_Superoxide_Dismutase 34 135 2.75593E-50
10 g16289.t9 Gene3D G3DSA:2.60.40.200 - 7 142 2.7E-48
2 g16289.t9 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 33 143 5.5E-52
3 g16289.t9 PANTHER PTHR10003:SF66 SUPEROXIDE DISMUTASE [CU-ZN] 33 143 5.5E-52
7 g16289.t9 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 33 55 1.4E-41
6 g16289.t9 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 69 78 1.4E-41
5 g16289.t9 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 88 110 1.4E-41
4 g16289.t9 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 113 139 1.4E-41
1 g16289.t9 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 20 138 2.1E-40
9 g16289.t9 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 127 138 -
8 g16289.t9 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 30 141 1.57E-45

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