General information for g13490.t54
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Extracellular superoxide dismutase [Cu-Zn].
Parent gene
- The parent gene g13490 is located on chr_1: 30457945..30461971 (- 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_1 | g13490 | g13490.t54 | TTS | g13490.t54 | 30456617 | 30456617 |
| chr_1 | g13490 | g13490.t54 | isoform | g13490.t54 | 30456647 | 30460600 |
| chr_1 | g13490 | g13490.t54 | exon | g13490.t54.exon1 | 30456647 | 30457129 |
| chr_1 | g13490 | g13490.t54 | cds | g13490.t54.CDS1 | 30457118 | 30457129 |
| chr_1 | g13490 | g13490.t54 | exon | g13490.t54.exon2 | 30457203 | 30457251 |
| chr_1 | g13490 | g13490.t54 | cds | g13490.t54.CDS2 | 30457203 | 30457251 |
| chr_1 | g13490 | g13490.t54 | exon | g13490.t54.exon3 | 30457522 | 30457803 |
| chr_1 | g13490 | g13490.t54 | cds | g13490.t54.CDS3 | 30457522 | 30457803 |
| chr_1 | g13490 | g13490.t54 | exon | g13490.t54.exon4 | 30457854 | 30457881 |
| chr_1 | g13490 | g13490.t54 | cds | g13490.t54.CDS4 | 30457854 | 30457867 |
| chr_1 | g13490 | g13490.t54 | exon | g13490.t54.exon5 | 30457941 | 30458040 |
| chr_1 | g13490 | g13490.t54 | exon | g13490.t54.exon6 | 30458178 | 30458342 |
| chr_1 | g13490 | g13490.t54 | exon | g13490.t54.exon7 | 30460580 | 30460600 |
| chr_1 | g13490 | g13490.t54 | TSS | g13490.t54 | 30460600 | 30460600 |
Sequences
>g13490.t54 Gene=g13490 Length=1128
AGTTTTGCGACAGAAGTTAAAATCAGTTGCAATCATTTCATTCAACATCAAAGACCTAAA
AATACGAGATGAAATCCTTAGTCATCATTTTCGTAATTTGTCTCTCAACAATCATCGTCA
ATGGCGATGAAGCGAAGCCTGCAAAAGCTATAGCAGTGCTTGGATTCTCAAACTCCGTCC
ATGGAAACATCACTTTCTCACAATCATCCTGTACGGAAGCAGTTCTCGTTCAAATTGAAA
TAACTGGCCTTACACCAGGCAAACACGGCTTTCATGTTCACGAAAAAGGCGATTTGTCGA
ATGGATGCACGTAAGAGCACAGGAAGTCATTTCAACCCAGATCGCTTGAATCATGGCGCA
CGTGAAGCACAAGTTCGTCACGTTGGTGATTTGGGCAACGTTGTTGCTGATGATCAAGGA
CGCGTCTCAACATCATTTTCGGATAATGTCATTACATTGTTTGGTGCTCGAAGTATCATT
GGTAGAGCAATTGTTGTTCACACCGATGAAGATGACCTTGGTCTTACCGATCATCAAGAC
TCTCATAAAACGGGAAATGCTGGTGGACGTGTTGCATGCGGAATTATTGGAATCTTGGAG
CCATCGAATGACGAATGGACATGTAATTCATCATCGAGAACACAACATACTCGCTAATTC
TAATGTTCGTTGTTGCTGTTATTGTTTGTGAAATGGAATTAAAGACAACTCATACACACA
CTCTGACACACACAGTCTTGTTGACCATTTGACACATTTTTATCATGAATATTCTTGTAT
TTGAATGAATATTTTGATTTATTAAAGTTGAAACTTGAAAACTCTTTTATACTCACAATT
TTTATTGTTTATTTATTTCTTGGTTTATATTTTTGATTTTTATAGACCTGATTATTTGTT
TATTAATGAATTAAACTATAAACTCACTTTAAAACAATCTAAATAGTAAAATTCAAAAAA
GCAGTTAAGATCAATTTTATTCACAATAAATTAATTTTGAGTGTAAATTTTCGACTAAAA
TTTTTCGTCGAGATTTAAATTATTCGGTCAGATTAAAAATAAATCTTTCCAAAATAAATC
GTAAGATTTGAGAATTAAATTTTTTTAAGAAAAAAATAAAATTGGACA
>g13490.t54 Gene=g13490 Length=118
MDARKSTGSHFNPDRLNHGAREAQVRHVGDLGNVVADDQGRVSTSFSDNVITLFGARSII
GRAIVVHTDEDDLGLTDHQDSHKTGNAGGRVACGIIGILEPSNDEWTCNSSSRTQHTR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13490.t54 | CDD | cd00305 | Cu-Zn_Superoxide_Dismutase | 5 | 93 | 6.82116E-34 |
| 9 | g13490.t54 | Gene3D | G3DSA:2.60.40.200 | - | 1 | 108 | 5.4E-37 |
| 2 | g13490.t54 | PANTHER | PTHR10003 | SUPEROXIDE DISMUTASE CU-ZN -RELATED | 5 | 100 | 5.7E-34 |
| 3 | g13490.t54 | PANTHER | PTHR10003:SF31 | SUPEROXIDE DISMUTASE [CU-ZN] 3 | 5 | 100 | 5.7E-34 |
| 4 | g13490.t54 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 27 | 36 | 1.8E-26 |
| 5 | g13490.t54 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 46 | 68 | 1.8E-26 |
| 6 | g13490.t54 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 71 | 97 | 1.8E-26 |
| 1 | g13490.t54 | Pfam | PF00080 | Copper/zinc superoxide dismutase (SODC) | 5 | 96 | 7.5E-29 |
| 8 | g13490.t54 | ProSitePatterns | PS00332 | Copper/Zinc superoxide dismutase signature 2. | 85 | 96 | - |
| 7 | g13490.t54 | SUPERFAMILY | SSF49329 | Cu,Zn superoxide dismutase-like | 5 | 98 | 3.8E-34 |
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