General information for g2209.t2
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.t2 | TSS | g2209.t2 | 16017010 | 16017010 |
| chr_3 | g2209 | g2209.t2 | isoform | g2209.t2 | 16017065 | 16018091 |
| chr_3 | g2209 | g2209.t2 | exon | g2209.t2.exon1 | 16017065 | 16017118 |
| chr_3 | g2209 | g2209.t2 | cds | g2209.t2.CDS1 | 16017065 | 16017118 |
| chr_3 | g2209 | g2209.t2 | exon | g2209.t2.exon2 | 16017360 | 16017498 |
| chr_3 | g2209 | g2209.t2 | cds | g2209.t2.CDS2 | 16017360 | 16017498 |
| chr_3 | g2209 | g2209.t2 | exon | g2209.t2.exon3 | 16017633 | 16018008 |
| chr_3 | g2209 | g2209.t2 | cds | g2209.t2.CDS3 | 16017633 | 16018008 |
| chr_3 | g2209 | g2209.t2 | exon | g2209.t2.exon4 | 16018081 | 16018091 |
| chr_3 | g2209 | g2209.t2 | cds | g2209.t2.CDS4 | 16018081 | 16018090 |
| chr_3 | g2209 | g2209.t2 | TTS | g2209.t2 | NA | NA |
Sequences
>g2209.t2 Gene=g2209 Length=580
ATGACTGGTCTCTTAAAGTGTTCTACATTATTAGCAAGAAACACACAGAACCTTCTAAAG
ACACTTTCGTTTACATCGTCAAGAAATCTTCATTTTACGGTCGGAAACAATAATTCCAAA
GCAAATCCAAATGCCATATCAAATGCTTATCAAGTAGTTGATCATGAATTTGACGCTGTT
GTCGTCGGTGCAGGCGGTGCTGGTCTTCGAGCTGCTTTTGGTCTCGTTGCCGAAGGTTTC
AAAACAGCTGTTGTGACAAAATTATTCCCCACACGATCACATACAGTTGCTGCACAAGGA
GGAATCAATGCAGCTCTCGGGAATATGGAACCCGATGACTGGAAATGGCACATGTATGAT
ACAGTTAAGGGATCAGATTGGTTAGGCGATCAAGATGCAATCAATTACATGACTCGCGAA
GCACCAAAAGCTGTTATTGAACTTGAAAATTATGGAATGCCATTCTCACGTACACCAGAT
GGAAAAATTTATCAACGTGCCTTTGGTGGTCAAAGTTATAACTATGGAAAAGGTGGTCAG
GCACATCGATGCTGTTGCGTTGCTGACAGAACCGGTCACT
>g2209.t2 Gene=g2209 Length=193
MTGLLKCSTLLARNTQNLLKTLSFTSSRNLHFTVGNNNSKANPNAISNAYQVVDHEFDAV
VVGAGGAGLRAAFGLVAEGFKTAVVTKLFPTRSHTVAAQGGINAALGNMEPDDWKWHMYD
TVKGSDWLGDQDAINYMTREAPKAVIELENYGMPFSRTPDGKIYQRAFGGQSYNYGKGGQ
AHRCCCVADRTGH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2209.t2 | Gene3D | G3DSA:3.50.50.60 | - | 39 | 193 | 2.3E-64 |
| 2 | g2209.t2 | PANTHER | PTHR11632 | SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT | 46 | 193 | 3.2E-87 |
| 3 | g2209.t2 | PANTHER | PTHR11632:SF51 | SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL | 46 | 193 | 3.2E-87 |
| 1 | g2209.t2 | Pfam | PF00890 | FAD binding domain | 58 | 192 | 9.2E-40 |
| 5 | g2209.t2 | ProSitePatterns | PS00504 | Fumarate reductase / succinate dehydrogenase FAD-binding site. | 92 | 101 | - |
| 4 | g2209.t2 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 48 | 189 | 1.76E-35 |
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.
