General information for g2209.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial.
Parent gene
- The parent gene g2209 is located on chr_3: 16019894..16020522 (+ 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_3 | g2209 | g2209.t9 | isoform | g2209.t9 | 16018907 | 16019512 |
| chr_3 | g2209 | g2209.t9 | exon | g2209.t9.exon1 | 16018907 | 16019512 |
| chr_3 | g2209 | g2209.t9 | cds | g2209.t9.CDS1 | 16018938 | 16019510 |
| chr_3 | g2209 | g2209.t9 | TTS | g2209.t9 | 16020530 | 16020530 |
| chr_3 | g2209 | g2209.t9 | TSS | g2209.t9 | NA | NA |
Sequences
>g2209.t9 Gene=g2209 Length=606
TTTGGCCTCACGTGATGTTGTCTCACGTTCAATGACAATTGAAATTCGTGAGGGAAGAGG
CTGTGGTCCCGAGAAAGACCACGTTTACTTGCAATTACACCATTTGCCCCCAGAACAATT
GGCTCAACGTTTGCCGGGTATCTCGGAAACTGCAATGATTTTTGCTGGTGTTGATGTTAC
ACGTGAGCCAATTCCTGTTCTCCCTACAGTTCACTATAACATGGGCGGTGTGCCAACAAA
TTACAAGGGTCAAGTGCTGACTATCGATAAGAAAGGAGATGATGTTATTGTACCTGGACT
TTATGCTTGTGGAGAAGCTGCATGCTCTTCTGTACATGGTGCTAATCGTTTAGGTGCAAA
TTCACTTTTAGATTTAGTTGTATTTGGACGTGCTTGTGCAAAGACAATCGCTGAAGAGAA
TAAACCAGGCGAGAAACTTCCCAATCTCCCTGATAATGCTGGTGAAGAATCCGTTGCTAA
TTTAGATTGGGTACGAAATGCAAGTGGTGCAGTACCAACTGCTGATTTGCGTTTGAAAAT
GCAGAAAACTATGCAAAATCACGCTGCTGTGTTCCGTGAAGCTAAAACACTCCAAGAGGG
TGTACA
>g2209.t9 Gene=g2209 Length=191
MTIEIREGRGCGPEKDHVYLQLHHLPPEQLAQRLPGISETAMIFAGVDVTREPIPVLPTV
HYNMGGVPTNYKGQVLTIDKKGDDVIVPGLYACGEAACSSVHGANRLGANSLLDLVVFGR
ACAKTIAEENKPGEKLPNLPDNAGEESVANLDWVRNASGAVPTADLRLKMQKTMQNHAAV
FREAKTLQEGV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2209.t9 | Gene3D | G3DSA:3.90.700.10 | Flavocytochrome C3; Chain A | 1 | 52 | 0e+00 |
| 9 | g2209.t9 | Gene3D | G3DSA:3.50.50.60 | - | 53 | 137 | 0e+00 |
| 8 | g2209.t9 | Gene3D | G3DSA:1.20.58.100 | - | 138 | 191 | 0e+00 |
| 2 | g2209.t9 | PANTHER | PTHR11632 | SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT | 1 | 191 | 0e+00 |
| 3 | g2209.t9 | PANTHER | PTHR11632:SF51 | SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL | 1 | 191 | 0e+00 |
| 1 | g2209.t9 | Pfam | PF00890 | FAD binding domain | 3 | 112 | 0e+00 |
| 4 | g2209.t9 | SUPERFAMILY | SSF56425 | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 2 | 62 | 0e+00 |
| 6 | g2209.t9 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 43 | 133 | 0e+00 |
| 5 | g2209.t9 | SUPERFAMILY | SSF46977 | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 159 | 191 | 9e-07 |
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:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
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.
