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.t137 TTS g13490.t137 30456939 30456939
chr_1 g13490 g13490.t137 isoform g13490.t137 30457118 30458344
chr_1 g13490 g13490.t137 exon g13490.t137.exon1 30457118 30457822
chr_1 g13490 g13490.t137 cds g13490.t137.CDS1 30457518 30457822
chr_1 g13490 g13490.t137 exon g13490.t137.exon2 30457941 30458040
chr_1 g13490 g13490.t137 cds g13490.t137.CDS2 30457941 30457953
chr_1 g13490 g13490.t137 exon g13490.t137.exon3 30458178 30458344
chr_1 g13490 g13490.t137 TSS g13490.t137 NA NA

Sequences

>g13490.t137 Gene=g13490 Length=972
AGATCAGTTGCAATCATTTCATTCAACATCAAAGACCTAAAAATACGAGATGAAATCCTT
AGTCATCATTTTCGTAATTTGTCTCTCAACAATCATCGTCAATGGCGATGAAGCGAAGCC
TGCAAAAGCTATAGCAGTGCTTGGATTCTCAAACTCCGTCCATGGAAACATCACTTTCTC
ACAATCATCCTGTACGGAAGCAGTTCTCGTTCAAATTGAAATAACTGGCCTTACACCAGG
CAAACACGGCTTTCATGTTCACGAAAATCTTATTTCTCACATATAGGAGCACAGGAAGTC
ATTTCAACCCAGATCGCTTGAATCATGGCGCACGTGAAGCACAAGTTCGTCACGTTGGTG
ATTTGGGCAACGTTGTTGCTGATGATCAAGGACGCGTCTCAACATCATTTTCGGATAATG
TCATTACATTGTTTGGTGCTCGAAGTATCATTGGTAGAGCAATTGTTGTTCACACCGATG
AAGATGACCTTGGTCTTACCGATCATCAAGACTCTCATAAAACGGGAAATGCTGGTGGAC
GTGTTGCATGCGGAATTATTGGAATCTTGTAAATATTTTTTTCTCTTTTCTCACTTTTCT
TATCATCATTTTTGCTTTTTATACATACACAAGAATAAGAAGAGAATTTCTGTTTAGTGA
GAATAAAAATAATTCTTAATCGTCATGTGTTCATTTGACCCTGTAAAAATGTTATTAACT
GTTGATGTGTGCGTGAGTAAAATGTATCAAGGTGAAGGTCATTTGCTCACACAATTGATA
GCTAAATGTGCATTTATCACTTGACTTTTTTGATCGAATGAATTTCAATCATTTACAGGG
AGCCATCGAATGACGAATGGACATGTAATTCATCATCGAGAACACAAGTGGGATTATTGT
TGATTCTCGTTATTATTGCTGTAATTAGAGCATAAACTCTTCTCTTTTATTTATTTGTAG
CATACTCGCTAA

>g13490.t137 Gene=g13490 Length=105
MFTKILFLTYRSTGSHFNPDRLNHGAREAQVRHVGDLGNVVADDQGRVSTSFSDNVITLF
GARSIIGRAIVVHTDEDDLGLTDHQDSHKTGNAGGRVACGIIGIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13490.t137 CDD cd00305 Cu-Zn_Superoxide_Dismutase 12 99 1.75307E-33
9 g13490.t137 Gene3D G3DSA:2.60.40.200 - 7 105 1.4E-36
2 g13490.t137 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 11 104 2.2E-33
3 g13490.t137 PANTHER PTHR10003:SF31 SUPEROXIDE DISMUTASE [CU-ZN] 3 11 104 2.2E-33
6 g13490.t137 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 33 42 1.5E-26
4 g13490.t137 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 52 74 1.5E-26
5 g13490.t137 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 77 103 1.5E-26
1 g13490.t137 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 11 102 4.3E-29
8 g13490.t137 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 91 102 -
7 g13490.t137 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 11 104 6.02E-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