Gene loci information

Transcript annotation

  • This transcript has been annotated as Superoxide dismutase [Mn], mitochondrial.

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_2 g7639 g7639.t12 TSS g7639.t12 25028506 25028506
chr_2 g7639 g7639.t12 isoform g7639.t12 25028585 25029400
chr_2 g7639 g7639.t12 exon g7639.t12.exon1 25028585 25028622
chr_2 g7639 g7639.t12 exon g7639.t12.exon2 25028742 25028821
chr_2 g7639 g7639.t12 cds g7639.t12.CDS1 25028816 25028821
chr_2 g7639 g7639.t12 exon g7639.t12.exon3 25028885 25029400
chr_2 g7639 g7639.t12 cds g7639.t12.CDS2 25028885 25029400
chr_2 g7639 g7639.t12 TTS g7639.t12 25029516 25029516

Sequences

>g7639.t12 Gene=g7639 Length=634
ATGTTGTCATTTTCACGTCAAGTCTTGCCTAAAGCCAGTCAGAACAAAAGCAACTTTGCC
GGAATTGCCATATGATTATGCTGCTCTTGAACCAATTGTTTGCCGTGAAATTATGGAGAT
TCATCATTCAAAACATCATCAAGCATACGTTACAAACTACAATGCAGCCAAAGAACAATT
AGATGAAGCAGTAGCAAAAGGAGATACAAATAAAATCATACAATTACAACCTGCTCTTCG
ATTCAACGGTGGTGGACATATCAATCACAGCATTTTCTGGAAGAATTTGTCACCGGAAAA
GACAACACCATCTGATGCTCTCAAGCAAGCAATTGTTAAAGATTTTAAATCAATTGATAA
TTTGAAAGCTGAGCTTAAAACAGCTGCTGTTGGTGTTCAAGGTAGCGGATGGGCATGGTT
AGGACTGAATAAGAAGACTGGAATTCTTCAAGTTGTGCAATGCGCTAATCAAGATCCTTT
GCAAGCAACAACCGGACTCGTTCCTTTATTTGGAATTGATGTTTGGGAACATGCATATTA
TCTGCAATATAAGAACCTTCGACCAAACTATGTCGATGCAATCTTCGATATTGTAAACTG
GAAAGATGTTTCTGAGCGATTCTCATCCGCTTAA

>g7639.t12 Gene=g7639 Length=173
MEIHHSKHHQAYVTNYNAAKEQLDEAVAKGDTNKIIQLQPALRFNGGGHINHSIFWKNLS
PEKTTPSDALKQAIVKDFKSIDNLKAELKTAAVGVQGSGWAWLGLNKKTGILQVVQCANQ
DPLQATTGLVPLFGIDVWEHAYYLQYKNLRPNYVDAIFDIVNWKDVSERFSSA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g7639.t12 Gene3D G3DSA:1.10.287.990 Fe 1 60 2.9E-28
12 g7639.t12 Gene3D G3DSA:2.40.500.20 - 61 173 4.1E-44
3 g7639.t12 PANTHER PTHR11404 SUPEROXIDE DISMUTASE 2 1 172 2.5E-75
13 g7639.t12 PIRSF PIRSF000349 MnSOD_FeSOD 1 173 4.5E-66
5 g7639.t12 PRINTS PR01703 Manganese superoxide dismutase signature 4 17 3.0E-20
7 g7639.t12 PRINTS PR01703 Manganese superoxide dismutase signature 43 56 3.0E-20
4 g7639.t12 PRINTS PR01703 Manganese superoxide dismutase signature 95 103 3.0E-20
6 g7639.t12 PRINTS PR01703 Manganese superoxide dismutase signature 134 146 3.0E-20
1 g7639.t12 Pfam PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain 1 60 9.7E-21
2 g7639.t12 Pfam PF02777 Iron/manganese superoxide dismutases, C-terminal domain 66 169 2.1E-35
10 g7639.t12 ProSitePatterns PS00088 Manganese and iron superoxide dismutases signature. 136 143 -
9 g7639.t12 SUPERFAMILY SSF46609 Fe,Mn superoxide dismutase (SOD), N-terminal domain 1 63 7.99E-23
8 g7639.t12 SUPERFAMILY SSF54719 Fe,Mn superoxide dismutase (SOD), C-terminal domain 62 171 4.32E-43

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