General information for g16289.t20
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 g16289 is located on chr_4: 8979839..8997574 (- 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 | g16289 | g16289.t20 | TTS | g16289.t20 | 8979680 | 8979680 |
| chr_4 | g16289 | g16289.t20 | isoform | g16289.t20 | 8979839 | 8980639 |
| chr_4 | g16289 | g16289.t20 | exon | g16289.t20.exon1 | 8979839 | 8980021 |
| chr_4 | g16289 | g16289.t20 | cds | g16289.t20.CDS1 | 8979839 | 8980021 |
| chr_4 | g16289 | g16289.t20 | exon | g16289.t20.exon2 | 8980123 | 8980232 |
| chr_4 | g16289 | g16289.t20 | cds | g16289.t20.CDS2 | 8980123 | 8980232 |
| chr_4 | g16289 | g16289.t20 | exon | g16289.t20.exon3 | 8980396 | 8980456 |
| chr_4 | g16289 | g16289.t20 | cds | g16289.t20.CDS3 | 8980396 | 8980456 |
| chr_4 | g16289 | g16289.t20 | exon | g16289.t20.exon4 | 8980577 | 8980639 |
| chr_4 | g16289 | g16289.t20 | cds | g16289.t20.CDS4 | 8980577 | 8980639 |
| chr_4 | g16289 | g16289.t20 | TSS | g16289.t20 | 8980729 | 8980729 |
Sequences
>g16289.t20 Gene=g16289 Length=417
ATGGTAAAAGCAGTTTGTGTAATGATAGGTGATGTCGAAGGAACATGTTTCTTTGAGCAA
GTTGATGGAAAAGGCCCAGTTCATATTACCGGTGAGGTCAAAGGTCTTAAACCTGGATTA
CATGGTTTTCACGTCCATGAATATGGTGACAATACCAATGGCTGCATGTCAGCTGGTCAA
CATTTCAATCCAACTAATAAAGATCATGGTGCACCGAATGTAGAAAATCGTCATGCTAAA
ATTGACATAACTGATAAAGTGATGTCTTTAAATGGAGAATTTAGTATTATTGGTCGAACA
ATGGTTGTCCACACTAATCCAGATGATTTGGGTGTTGGTGGTGCAGAAACATCAAAGAAA
GACGGTAACGCTGGTGGCCGCCTGGCTTGCGGCGTTATTGGCATCTGCAAGGCATAA
>g16289.t20 Gene=g16289 Length=138
MVKAVCVMIGDVEGTCFFEQVDGKGPVHITGEVKGLKPGLHGFHVHEYGDNTNGCMSAGQ
HFNPTNKDHGAPNVENRHAKIDITDKVMSLNGEFSIIGRTMVVHTNPDDLGVGGAETSKK
DGNAGGRLACGVIGICKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g16289.t20 | CDD | cd00305 | Cu-Zn_Superoxide_Dismutase | 2 | 130 | 2.32647E-50 |
| 7 | g16289.t20 | Gene3D | G3DSA:2.60.40.200 | - | 1 | 77 | 2.2E-26 |
| 8 | g16289.t20 | Gene3D | G3DSA:2.60.40.200 | - | 78 | 137 | 5.6E-19 |
| 2 | g16289.t20 | PANTHER | PTHR10003 | SUPEROXIDE DISMUTASE CU-ZN -RELATED | 2 | 138 | 5.2E-50 |
| 3 | g16289.t20 | PANTHER | PTHR10003:SF66 | SUPEROXIDE DISMUTASE [CU-ZN] | 2 | 138 | 5.2E-50 |
| 1 | g16289.t20 | Pfam | PF00080 | Copper/zinc superoxide dismutase (SODC) | 10 | 133 | 6.4E-35 |
| 6 | g16289.t20 | ProSitePatterns | PS00087 | Copper/Zinc superoxide dismutase signature 1. | 42 | 52 | - |
| 5 | g16289.t20 | ProSitePatterns | PS00332 | Copper/Zinc superoxide dismutase signature 2. | 122 | 133 | - |
| 4 | g16289.t20 | SUPERFAMILY | SSF49329 | Cu,Zn superoxide dismutase-like | 4 | 136 | 6.15E-46 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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