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.t14 TSS g7639.t14 25028506 25028506
chr_2 g7639 g7639.t14 isoform g7639.t14 25028585 25029400
chr_2 g7639 g7639.t14 exon g7639.t14.exon1 25028585 25028622
chr_2 g7639 g7639.t14 exon g7639.t14.exon2 25028722 25028807
chr_2 g7639 g7639.t14 cds g7639.t14.CDS1 25028775 25028807
chr_2 g7639 g7639.t14 exon g7639.t14.exon3 25028885 25029400
chr_2 g7639 g7639.t14 cds g7639.t14.CDS2 25028885 25029400
chr_2 g7639 g7639.t14 TTS g7639.t14 25029516 25029516

Sequences

>g7639.t14 Gene=g7639 Length=640
ATGTTGTCATTTTCACGTCAAGTCTTGCCTAAAGCCAGAAATATGGCGCTCACAACAGTC
AGAACAAAAGCAACTTTGCCGGAATTGCCATATGATTATGCTGCTCTTGAACCAATTGTT
TGCCATTCATCATTCAAAACATCATCAAGCATACGTTACAAACTACAATGCAGCCAAAGA
ACAATTAGATGAAGCAGTAGCAAAAGGAGATACAAATAAAATCATACAATTACAACCTGC
TCTTCGATTCAACGGTGGTGGACATATCAATCACAGCATTTTCTGGAAGAATTTGTCACC
GGAAAAGACAACACCATCTGATGCTCTCAAGCAAGCAATTGTTAAAGATTTTAAATCAAT
TGATAATTTGAAAGCTGAGCTTAAAACAGCTGCTGTTGGTGTTCAAGGTAGCGGATGGGC
ATGGTTAGGACTGAATAAGAAGACTGGAATTCTTCAAGTTGTGCAATGCGCTAATCAAGA
TCCTTTGCAAGCAACAACCGGACTCGTTCCTTTATTTGGAATTGATGTTTGGGAACATGC
ATATTATCTGCAATATAAGAACCTTCGACCAAACTATGTCGATGCAATCTTCGATATTGT
AAACTGGAAAGATGTTTCTGAGCGATTCTCATCCGCTTAA

>g7639.t14 Gene=g7639 Length=182
MIMLLLNQLFAIHHSKHHQAYVTNYNAAKEQLDEAVAKGDTNKIIQLQPALRFNGGGHIN
HSIFWKNLSPEKTTPSDALKQAIVKDFKSIDNLKAELKTAAVGVQGSGWAWLGLNKKTGI
LQVVQCANQDPLQATTGLVPLFGIDVWEHAYYLQYKNLRPNYVDAIFDIVNWKDVSERFS
SA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g7639.t14 Gene3D G3DSA:1.10.287.990 Fe 7 69 3.6E-27
12 g7639.t14 Gene3D G3DSA:2.40.500.20 - 70 182 4.7E-44
3 g7639.t14 PANTHER PTHR11404 SUPEROXIDE DISMUTASE 2 7 181 5.4E-75
13 g7639.t14 PIRSF PIRSF000349 MnSOD_FeSOD 3 182 7.1E-66
4 g7639.t14 PRINTS PR01703 Manganese superoxide dismutase signature 13 26 3.4E-20
7 g7639.t14 PRINTS PR01703 Manganese superoxide dismutase signature 52 65 3.4E-20
5 g7639.t14 PRINTS PR01703 Manganese superoxide dismutase signature 104 112 3.4E-20
6 g7639.t14 PRINTS PR01703 Manganese superoxide dismutase signature 143 155 3.4E-20
1 g7639.t14 Pfam PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain 8 69 2.3E-20
2 g7639.t14 Pfam PF02777 Iron/manganese superoxide dismutases, C-terminal domain 75 178 2.4E-35
10 g7639.t14 ProSitePatterns PS00088 Manganese and iron superoxide dismutases signature. 145 152 -
9 g7639.t14 SUPERFAMILY SSF46609 Fe,Mn superoxide dismutase (SOD), N-terminal domain 7 72 1.44E-22
8 g7639.t14 SUPERFAMILY SSF54719 Fe,Mn superoxide dismutase (SOD), C-terminal domain 71 180 4.98E-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