General information for g16280.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Superoxide dismutase [Cu-Zn].
Parent gene
- The parent gene g16280 is located on chr_4: 8956959..8965285 (- strand)
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_4 | g16280 | g16280.t1 | TTS | g16280.t1 | 8956500 | 8956500 |
| chr_4 | g16280 | g16280.t1 | isoform | g16280.t1 | 8956673 | 8957463 |
| chr_4 | g16280 | g16280.t1 | exon | g16280.t1.exon1 | 8956673 | 8956897 |
| chr_4 | g16280 | g16280.t1 | cds | g16280.t1.CDS1 | 8956673 | 8956897 |
| chr_4 | g16280 | g16280.t1 | exon | g16280.t1.exon2 | 8956961 | 8957070 |
| chr_4 | g16280 | g16280.t1 | cds | g16280.t1.CDS2 | 8956961 | 8957070 |
| chr_4 | g16280 | g16280.t1 | exon | g16280.t1.exon3 | 8957152 | 8957206 |
| chr_4 | g16280 | g16280.t1 | cds | g16280.t1.CDS3 | 8957152 | 8957206 |
| chr_4 | g16280 | g16280.t1 | exon | g16280.t1.exon4 | 8957356 | 8957463 |
| chr_4 | g16280 | g16280.t1 | cds | g16280.t1.CDS4 | 8957356 | 8957463 |
| chr_4 | g16280 | g16280.t1 | TSS | g16280.t1 | 8957532 | 8957532 |
Sequences
>g16280.t1 Gene=g16280 Length=498
ATGGATAAGTTAAAAAAAGCATTAGATATTGAAAAAGATCATCCAGTTACAAGAGCTGTT
TGTGTCATGATTGGTGAAGCTGAAGGAACTTGCTACTTTGAACAAGCTAAGGGTCCCGTT
CATATCACTGGTGAAATCAAAGGTTTAAAACCTGGCTTGCATGGTTTTCATATCCATGAA
TATGGTGACATTACCAACGGATGTATGTCTGCCGGACAGCATTTCAATCCATACAACAAA
CAACATGGAGGAACTCTTGATGACAATCGTCATGTTGGTGATTTGGGAAATATTAAAGCT
GAAGAAAATGGAATTGCAAAAATTGACATAACAGATCGAATGATTTCTCTGCATGGAAAC
TCGAATATTATTGGTCGCACGTTGGTTGTACATGTAAATGCCGACGATTTGGGACTTGGG
TCCAATGAACAATCAAAATCCGACGGTAACTCTGGTGGAAGAATTAGCTGTGGTGTTATT
GGCATCTGCAAGGCATAA
>g16280.t1 Gene=g16280 Length=165
MDKLKKALDIEKDHPVTRAVCVMIGEAEGTCYFEQAKGPVHITGEIKGLKPGLHGFHIHE
YGDITNGCMSAGQHFNPYNKQHGGTLDDNRHVGDLGNIKAEENGIAKIDITDRMISLHGN
SNIIGRTLVVHVNADDLGLGSNEQSKSDGNSGGRISCGVIGICKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g16280.t1 | CDD | cd00305 | Cu-Zn_Superoxide_Dismutase | 17 | 157 | 3.43149E-59 |
| 11 | g16280.t1 | Gene3D | G3DSA:2.60.40.200 | - | 18 | 164 | 3.1E-57 |
| 2 | g16280.t1 | PANTHER | PTHR10003 | SUPEROXIDE DISMUTASE CU-ZN -RELATED | 16 | 165 | 1.2E-59 |
| 3 | g16280.t1 | PANTHER | PTHR10003:SF66 | SUPEROXIDE DISMUTASE [CU-ZN] | 16 | 165 | 1.2E-59 |
| 4 | g16280.t1 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 55 | 77 | 8.4E-41 |
| 5 | g16280.t1 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 91 | 100 | 8.4E-41 |
| 6 | g16280.t1 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 110 | 132 | 8.4E-41 |
| 7 | g16280.t1 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 135 | 161 | 8.4E-41 |
| 1 | g16280.t1 | Pfam | PF00080 | Copper/zinc superoxide dismutase (SODC) | 26 | 160 | 6.6E-47 |
| 10 | g16280.t1 | ProSitePatterns | PS00087 | Copper/Zinc superoxide dismutase signature 1. | 55 | 65 | - |
| 9 | g16280.t1 | ProSitePatterns | PS00332 | Copper/Zinc superoxide dismutase signature 2. | 149 | 160 | - |
| 8 | g16280.t1 | SUPERFAMILY | SSF49329 | Cu,Zn superoxide dismutase-like | 17 | 163 | 2.09E-52 |
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 transcript has been annotated with K04565 (superoxide dismutase, Cu-Zn family)
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.
