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_1 g13490 g13490.t196 TTS g13490.t196 30456939 30456939
chr_1 g13490 g13490.t196 isoform g13490.t196 30457441 30460600
chr_1 g13490 g13490.t196 exon g13490.t196.exon1 30457441 30457800
chr_1 g13490 g13490.t196 cds g13490.t196.CDS1 30457518 30457800
chr_1 g13490 g13490.t196 exon g13490.t196.exon2 30457854 30457881
chr_1 g13490 g13490.t196 cds g13490.t196.CDS2 30457854 30457881
chr_1 g13490 g13490.t196 exon g13490.t196.exon3 30457941 30458040
chr_1 g13490 g13490.t196 cds g13490.t196.CDS3 30457941 30457953
chr_1 g13490 g13490.t196 exon g13490.t196.exon4 30458178 30458342
chr_1 g13490 g13490.t196 exon g13490.t196.exon5 30460580 30460600
chr_1 g13490 g13490.t196 TSS g13490.t196 30460600 30460600

Sequences

>g13490.t196 Gene=g13490 Length=674
AGTTTTGCGACAGAAGTTAAAATCAGTTGCAATCATTTCATTCAACATCAAAGACCTAAA
AATACGAGATGAAATCCTTAGTCATCATTTTCGTAATTTGTCTCTCAACAATCATCGTCA
ATGGCGATGAAGCGAAGCCTGCAAAAGCTATAGCAGTGCTTGGATTCTCAAACTCCGTCC
ATGGAAACATCACTTTCTCACAATCATCCTGTACGGAAGCAGTTCTCGTTCAAATTGAAA
TAACTGGCCTTACACCAGGCAAACACGGCTTTCATGTTCACGAAAAAGGCGATTTGTCGA
ATGGATGCACGTAACACAGGAAGTCATTTCAACCCAGATCGCTTGAATCATGGCGCACGT
GAAGCACAAGTTCGTCACGTTGGTGATTTGGGCAACGTTGTTGCTGATGATCAAGGACGC
GTCTCAACATCATTTTCGGATAATGTCATTACATTGTTTGGTGCTCGAAGTATCATTGGT
AGAGCAATTGTTGTTCACACCGATGAAGATGACCTTGGTCTTACCGATCATCAAGACTCT
CATAAAACGGGAAATGCTGGTGGACGTGTTGCATGCGGAATTATTGGAATCTTGTAAATA
TTTTTTTCTCTTTTCTCACTTTTCTTATCATCATTTTTGCTTTTTATACATACACAAGAA
TAAGAAGAGAATTT

>g13490.t196 Gene=g13490 Length=107
MFTKKAICRMDARNTGSHFNPDRLNHGAREAQVRHVGDLGNVVADDQGRVSTSFSDNVIT
LFGARSIIGRAIVVHTDEDDLGLTDHQDSHKTGNAGGRVACGIIGIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13490.t196 Gene3D G3DSA:2.60.40.200 - 3 107 1.2E-36
2 g13490.t196 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 12 106 1.2E-32
3 g13490.t196 PANTHER PTHR10003:SF31 SUPEROXIDE DISMUTASE [CU-ZN] 3 12 106 1.2E-32
6 g13490.t196 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 35 44 1.6E-26
5 g13490.t196 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 54 76 1.6E-26
4 g13490.t196 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 79 105 1.6E-26
1 g13490.t196 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 8 104 5.5E-29
8 g13490.t196 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 93 104 -
7 g13490.t196 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 6 106 2.09E-34

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