General information for g4810.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Copper chaperone for superoxide dismutase.
Parent gene
- The parent gene g4810 is located on chr_2: 5066638..5068674 (+ 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_2 | g4810 | g4810.t1 | TSS | g4810.t1 | 5066558 | 5066558 |
| chr_2 | g4810 | g4810.t1 | isoform | g4810.t1 | 5066638 | 5067324 |
| chr_2 | g4810 | g4810.t1 | exon | g4810.t1.exon1 | 5066638 | 5067324 |
| chr_2 | g4810 | g4810.t1 | cds | g4810.t1.CDS1 | 5066638 | 5067324 |
| chr_2 | g4810 | g4810.t1 | TTS | g4810.t1 | 5067354 | 5067354 |
Sequences
>g4810.t1 Gene=g4810 Length=687
ATGTCATCAGAAGAGAATTTGACAAGAGTTGAATTTGCAGTCAAAGTCAAAGATGAGAAA
GCTTTAAATAGAGTAAAATCATCATTAATTAATGAGGGTCAGATTGCCGAAAAAAATATT
GAAAGTATTGTTGATGCTGGTGAGGCAAGAATAGTTTGCAAGACAAATATACCATGGATT
TCATTGCATGAAATCATCGAAAAAACTGGATATGAATCTGCATTAGTGGGATTTAGTGAT
CAATCAGCTGTCACAATACTTGATGAAAGAAAGTTAACAAATATTAAAGGAGTTGTTCGA
TTTTGCAGTAGTCAGAAATCAATAATAGTCATTGATGGTGTAATTGACGGATTGAAAGAG
AACAAAGAACATAAATTTGGCATTTATGAGTATGGTGATTTGAGTGATGGATGTAATAAT
TTAGGAGAAGTTTACAAAAACGCAATATATAATGTCAATAGCAACGATAAAGGACGAATT
GTATTACGAAGAACAACAGACAATGATTTGACAATTTCTGATATAATTGGACGAGGAGTT
TGCATTTCAAATGATTCCGGTGAGAAACTTGCATGTGGTGTAATAAGTAGATCGGCAGGA
GTGTTTCAAAATTTTAAGAGAATTTGTCTCTGCTCAGGAAAATTGTTATGGGATGAGAGA
GATTTACAGAATATTGTAAAAAAATAA
>g4810.t1 Gene=g4810 Length=228
MSSEENLTRVEFAVKVKDEKALNRVKSSLINEGQIAEKNIESIVDAGEARIVCKTNIPWI
SLHEIIEKTGYESALVGFSDQSAVTILDERKLTNIKGVVRFCSSQKSIIVIDGVIDGLKE
NKEHKFGIYEYGDLSDGCNNLGEVYKNAIYNVNSNDKGRIVLRRTTDNDLTISDIIGRGV
CISNDSGEKLACGVISRSAGVFQNFKRICLCSGKLLWDERDLQNIVKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4810.t1 | Gene3D | G3DSA:2.60.40.200 | - | 81 | 197 | 0 |
| 2 | g4810.t1 | PANTHER | PTHR10003 | SUPEROXIDE DISMUTASE CU-ZN -RELATED | 15 | 221 | 0 |
| 3 | g4810.t1 | PANTHER | PTHR10003:SF88 | COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE | 15 | 221 | 0 |
| 1 | g4810.t1 | Pfam | PF00080 | Copper/zinc superoxide dismutase (SODC) | 93 | 195 | 0 |
| 4 | g4810.t1 | SUPERFAMILY | SSF49329 | Cu,Zn superoxide dismutase-like | 82 | 221 | 0 |
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:0046872 | metal ion binding | MF |
KEGG
Orthology
- This transcript has been annotated with K04569 (copper chaperone for superoxide dismutase)
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.
