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.t1 TSS g7639.t1 25028506 25028506
chr_2 g7639 g7639.t1 isoform g7639.t1 25028585 25029400
chr_2 g7639 g7639.t1 exon g7639.t1.exon1 25028585 25028622
chr_2 g7639 g7639.t1 cds g7639.t1.CDS1 25028585 25028622
chr_2 g7639 g7639.t1 exon g7639.t1.exon2 25028722 25028821
chr_2 g7639 g7639.t1 cds g7639.t1.CDS2 25028722 25028821
chr_2 g7639 g7639.t1 exon g7639.t1.exon3 25028885 25029400
chr_2 g7639 g7639.t1 cds g7639.t1.CDS3 25028885 25029400
chr_2 g7639 g7639.t1 TTS g7639.t1 25029516 25029516

Sequences

>g7639.t1 Gene=g7639 Length=654
ATGTTGTCATTTTCACGTCAAGTCTTGCCTAAAGCCAGAAATATGGCGCTCACAACAGTC
AGAACAAAAGCAACTTTGCCGGAATTGCCATATGATTATGCTGCTCTTGAACCAATTGTT
TGCCGTGAAATTATGGAGATTCATCATTCAAAACATCATCAAGCATACGTTACAAACTAC
AATGCAGCCAAAGAACAATTAGATGAAGCAGTAGCAAAAGGAGATACAAATAAAATCATA
CAATTACAACCTGCTCTTCGATTCAACGGTGGTGGACATATCAATCACAGCATTTTCTGG
AAGAATTTGTCACCGGAAAAGACAACACCATCTGATGCTCTCAAGCAAGCAATTGTTAAA
GATTTTAAATCAATTGATAATTTGAAAGCTGAGCTTAAAACAGCTGCTGTTGGTGTTCAA
GGTAGCGGATGGGCATGGTTAGGACTGAATAAGAAGACTGGAATTCTTCAAGTTGTGCAA
TGCGCTAATCAAGATCCTTTGCAAGCAACAACCGGACTCGTTCCTTTATTTGGAATTGAT
GTTTGGGAACATGCATATTATCTGCAATATAAGAACCTTCGACCAAACTATGTCGATGCA
ATCTTCGATATTGTAAACTGGAAAGATGTTTCTGAGCGATTCTCATCCGCTTAA

>g7639.t1 Gene=g7639 Length=217
MLSFSRQVLPKARNMALTTVRTKATLPELPYDYAALEPIVCREIMEIHHSKHHQAYVTNY
NAAKEQLDEAVAKGDTNKIIQLQPALRFNGGGHINHSIFWKNLSPEKTTPSDALKQAIVK
DFKSIDNLKAELKTAAVGVQGSGWAWLGLNKKTGILQVVQCANQDPLQATTGLVPLFGID
VWEHAYYLQYKNLRPNYVDAIFDIVNWKDVSERFSSA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g7639.t1 Gene3D G3DSA:1.10.287.990 Fe 41 104 4.3E-30
14 g7639.t1 Gene3D G3DSA:2.40.500.20 - 105 217 7.6E-44
3 g7639.t1 PANTHER PTHR11404 SUPEROXIDE DISMUTASE 2 21 215 5.1E-85
4 g7639.t1 PANTHER PTHR11404:SF6 SUPEROXIDE DISMUTASE [MN], MITOCHONDRIAL 21 215 5.1E-85
15 g7639.t1 PIRSF PIRSF000349 MnSOD_FeSOD 2 217 1.9E-76
8 g7639.t1 PRINTS PR01703 Manganese superoxide dismutase signature 27 38 2.9E-27
9 g7639.t1 PRINTS PR01703 Manganese superoxide dismutase signature 48 61 2.9E-27
5 g7639.t1 PRINTS PR01703 Manganese superoxide dismutase signature 87 100 2.9E-27
7 g7639.t1 PRINTS PR01703 Manganese superoxide dismutase signature 139 147 2.9E-27
6 g7639.t1 PRINTS PR01703 Manganese superoxide dismutase signature 178 190 2.9E-27
1 g7639.t1 Pfam PF00081 Iron/manganese superoxide dismutases, alpha-hairpin domain 25 104 4.4E-33
2 g7639.t1 Pfam PF02777 Iron/manganese superoxide dismutases, C-terminal domain 110 213 3.8E-35
12 g7639.t1 ProSitePatterns PS00088 Manganese and iron superoxide dismutases signature. 180 187 -
11 g7639.t1 SUPERFAMILY SSF46609 Fe,Mn superoxide dismutase (SOD), N-terminal domain 16 105 7.33E-35
10 g7639.t1 SUPERFAMILY SSF54719 Fe,Mn superoxide dismutase (SOD), C-terminal domain 106 215 7.99E-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