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.t16 TSS g7639.t16 25028506 25028506
chr_2 g7639 g7639.t16 isoform g7639.t16 25028885 25029518
chr_2 g7639 g7639.t16 exon g7639.t16.exon1 25028885 25029518
chr_2 g7639 g7639.t16 cds g7639.t16.CDS1 25028885 25029400
chr_2 g7639 g7639.t16 TTS g7639.t16 25029516 25029516

Sequences

>g7639.t16 Gene=g7639 Length=634
ATTCATCATTCAAAACATCATCAAGCATACGTTACAAACTACAATGCAGCCAAAGAACAA
TTAGATGAAGCAGTAGCAAAAGGAGATACAAATAAAATCATACAATTACAACCTGCTCTT
CGATTCAACGGTGGTGGACATATCAATCACAGCATTTTCTGGAAGAATTTGTCACCGGAA
AAGACAACACCATCTGATGCTCTCAAGCAAGCAATTGTTAAAGATTTTAAATCAATTGAT
AATTTGAAAGCTGAGCTTAAAACAGCTGCTGTTGGTGTTCAAGGTAGCGGATGGGCATGG
TTAGGACTGAATAAGAAGACTGGAATTCTTCAAGTTGTGCAATGCGCTAATCAAGATCCT
TTGCAAGCAACAACCGGACTCGTTCCTTTATTTGGAATTGATGTTTGGGAACATGCATAT
TATCTGCAATATAAGAACCTTCGACCAAACTATGTCGATGCAATCTTCGATATTGTAAAC
TGGAAAGATGTTTCTGAGCGATTCTCATCCGCTTAATTTGTATATATCGTATCGTATATT
TGAAATAGTTTTGCGAATCGCAAATCATTGTCGTCGATTTATATAATTGACACTTATGAA
TGAATAAAGAAACTCACTCAACTGATTGTATAAA

>g7639.t16 Gene=g7639 Length=171
IHHSKHHQAYVTNYNAAKEQLDEAVAKGDTNKIIQLQPALRFNGGGHINHSIFWKNLSPE
KTTPSDALKQAIVKDFKSIDNLKAELKTAAVGVQGSGWAWLGLNKKTGILQVVQCANQDP
LQATTGLVPLFGIDVWEHAYYLQYKNLRPNYVDAIFDIVNWKDVSERFSSA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g7639.t16 Gene3D G3DSA:1.10.287.990 Fe 1 58 1.4E-26
12 g7639.t16 Gene3D G3DSA:2.40.500.20 - 59 171 3.9E-44
3 g7639.t16 PANTHER PTHR11404 SUPEROXIDE DISMUTASE 2 1 170 4.5E-74
13 g7639.t16 PIRSF PIRSF000349 MnSOD_FeSOD 1 171 5.9E-65
7 g7639.t16 PRINTS PR01703 Manganese superoxide dismutase signature 2 15 2.9E-20
6 g7639.t16 PRINTS PR01703 Manganese superoxide dismutase signature 41 54 2.9E-20
5 g7639.t16 PRINTS PR01703 Manganese superoxide dismutase signature 93 101 2.9E-20
4 g7639.t16 PRINTS PR01703 Manganese superoxide dismutase signature 132 144 2.9E-20
1 g7639.t16 Pfam PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain 1 58 2.6E-19
2 g7639.t16 Pfam PF02777 Iron/manganese superoxide dismutases, C-terminal domain 64 167 2.0E-35
10 g7639.t16 ProSitePatterns PS00088 Manganese and iron superoxide dismutases signature. 134 141 -
9 g7639.t16 SUPERFAMILY SSF46609 Fe,Mn superoxide dismutase (SOD), N-terminal domain 1 61 1.7E-21
8 g7639.t16 SUPERFAMILY SSF54719 Fe,Mn superoxide dismutase (SOD), C-terminal domain 60 169 4.19E-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.

Raw TPM values