General information for g2209.t4
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.t4 | TSS | g2209.t4 | 16017010 | 16017010 |
| chr_3 | g2209 | g2209.t4 | isoform | g2209.t4 | 16017065 | 16019262 |
| chr_3 | g2209 | g2209.t4 | exon | g2209.t4.exon1 | 16017065 | 16017118 |
| chr_3 | g2209 | g2209.t4 | cds | g2209.t4.CDS1 | 16017065 | 16017118 |
| chr_3 | g2209 | g2209.t4 | exon | g2209.t4.exon2 | 16017360 | 16017492 |
| chr_3 | g2209 | g2209.t4 | cds | g2209.t4.CDS2 | 16017360 | 16017492 |
| chr_3 | g2209 | g2209.t4 | exon | g2209.t4.exon3 | 16017633 | 16018008 |
| chr_3 | g2209 | g2209.t4 | cds | g2209.t4.CDS3 | 16017633 | 16018008 |
| chr_3 | g2209 | g2209.t4 | exon | g2209.t4.exon4 | 16018081 | 16018233 |
| chr_3 | g2209 | g2209.t4 | cds | g2209.t4.CDS4 | 16018081 | 16018233 |
| chr_3 | g2209 | g2209.t4 | exon | g2209.t4.exon5 | 16018637 | 16019262 |
| chr_3 | g2209 | g2209.t4 | cds | g2209.t4.CDS5 | 16018637 | 16019261 |
| chr_3 | g2209 | g2209.t4 | TTS | g2209.t4 | NA | NA |
Sequences
>g2209.t4 Gene=g2209 Length=1342
ATGACTGGTCTCTTAAAGTGTTCTACATTATTAGCAAGAAACACACAGAACCTTCTAAAG
ACACTTTCGTTTACATCGTCAAGAAATCTTCATTTTACGGTCGGAAACAATAATTCCAAA
GCAAATCCAAATGCCATATCAAATGCTTATCAAGTAGTTGATCATGAATTTGACGCTGTT
GTCGTCGGCGGTGCTGGTCTTCGAGCTGCTTTTGGTCTCGTTGCCGAAGGTTTCAAAACA
GCTGTTGTGACAAAATTATTCCCCACACGATCACATACAGTTGCTGCACAAGGAGGAATC
AATGCAGCTCTCGGGAATATGGAACCCGATGACTGGAAATGGCACATGTATGATACAGTT
AAGGGATCAGATTGGTTAGGCGATCAAGATGCAATCAATTACATGACTCGCGAAGCACCA
AAAGCTGTTATTGAACTTGAAAATTATGGAATGCCATTCTCACGTACACCAGATGGAAAA
ATTTATCAACGTGCCTTTGGTGGTCAAAGTTATAACTATGGAAAAGGTGGTCAGGCACAT
CGATGCTGTTGCGTTGCTGACAGAACCGGTCACTCGCTTCTACACACTCTCTATGGTCAA
TCCCTTAGCTACAATTGCAACTATTTTATCGAATATTTTGCTATGGATTTAATTATGCAA
AATGGTGAATGCCATGGCGTTATTGCCTTAAACTTAGAAGATGGAACAATTCATCGTTTC
CGAGCAAAGAATACAGTACTCGCAACTGGCGGTTATGGACGTGCATATTTCTCTTGCACA
TCAGCACATACGTGTACTGGTGATGGCACTGCTATGGTGGCTCGTGCTGGTCTTCCTTCA
GAAGACTTGGAATTTGTGCAATTTCATCCAACCGGTATCTATGGTGCTGGTTGTTTGATT
ACAGAAGGTTGTCGCGGTGAAGGAGGCTATTTAATTAATTCACAAGGAGAACGTTTTATG
GAACGTTATGCTCCAGTTGCTAAGGATTTGGCCTCACGTGATGTTGTCTCACGTTCAATG
ACAATTGAAATTCGTGAGGGAAGAGGCTGTGGTCCCGAGAAAGACCACGTTTACTTGCAA
TTACACCATTTGCCCCCAGAACAATTGGCTCAACGTTTGCCGGGTATCTCGGAAACTGCA
ATGATTTTTGCTGGTGTTGATGTTACACGTGAGCCAATTCCTGTTCTCCCTACAGTTCAC
TATAACATGGGCGGTGTGCCAACAAATTACAAGGGTCAAGTGCTGACTATCGATAAGAAA
GGAGATGATGTTATTGTACCTGGACTTTATGCTTGTGGAGAAGCTGCATGCTCTTCTGTA
CATGGTGCTAATCGTTTAGGTG
>g2209.t4 Gene=g2209 Length=447
MTGLLKCSTLLARNTQNLLKTLSFTSSRNLHFTVGNNNSKANPNAISNAYQVVDHEFDAV
VVGGAGLRAAFGLVAEGFKTAVVTKLFPTRSHTVAAQGGINAALGNMEPDDWKWHMYDTV
KGSDWLGDQDAINYMTREAPKAVIELENYGMPFSRTPDGKIYQRAFGGQSYNYGKGGQAH
RCCCVADRTGHSLLHTLYGQSLSYNCNYFIEYFAMDLIMQNGECHGVIALNLEDGTIHRF
RAKNTVLATGGYGRAYFSCTSAHTCTGDGTAMVARAGLPSEDLEFVQFHPTGIYGAGCLI
TEGCRGEGGYLINSQGERFMERYAPVAKDLASRDVVSRSMTIEIREGRGCGPEKDHVYLQ
LHHLPPEQLAQRLPGISETAMIFAGVDVTREPIPVLPTVHYNMGGVPTNYKGQVLTIDKK
GDDVIVPGLYACGEAACSSVHGANRLG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2209.t4 | Gene3D | G3DSA:3.50.50.60 | - | 58 | 447 | 1.0E-164 |
| 7 | g2209.t4 | Gene3D | G3DSA:3.90.700.10 | Flavocytochrome C3; Chain A | 293 | 396 | 1.0E-164 |
| 2 | g2209.t4 | PANTHER | PTHR11632 | SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT | 47 | 447 | 1.1E-246 |
| 3 | g2209.t4 | PANTHER | PTHR11632:SF51 | SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL | 47 | 447 | 1.1E-246 |
| 1 | g2209.t4 | Pfam | PF00890 | FAD binding domain | 58 | 447 | 3.0E-123 |
| 6 | g2209.t4 | ProSitePatterns | PS00504 | Fumarate reductase / succinate dehydrogenase FAD-binding site. | 90 | 99 | - |
| 5 | g2209.t4 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 49 | 436 | 1.61E-68 |
| 4 | g2209.t4 | SUPERFAMILY | SSF56425 | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 283 | 401 | 1.29E-42 |
| 9 | g2209.t4 | TIGRFAM | TIGR01816 | sdhA_forward: succinate dehydrogenase, flavoprotein subunit | 55 | 447 | 4.9E-227 |
| 10 | g2209.t4 | TIGRFAM | TIGR01812 | sdhA_frdA_Gneg: succinate dehydrogenase or fumarate reductase, flavoprotein subunit | 58 | 447 | 1.0E-178 |
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:0016627 | oxidoreductase activity, acting on the CH-CH group of donors | MF |
| GO:0006099 | tricarboxylic acid cycle | BP |
| GO:0022900 | electron transport chain | BP |
| GO:0050660 | flavin adenine dinucleotide binding | MF |
| 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. There were no conditions that were differentially expressed