General information for g2209.t1
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.t1 | TSS | g2209.t1 | 16017010 | 16017010 |
| chr_3 | g2209 | g2209.t1 | isoform | g2209.t1 | 16017065 | 16019894 |
| chr_3 | g2209 | g2209.t1 | exon | g2209.t1.exon1 | 16017065 | 16017118 |
| chr_3 | g2209 | g2209.t1 | cds | g2209.t1.CDS1 | 16017065 | 16017118 |
| chr_3 | g2209 | g2209.t1 | exon | g2209.t1.exon2 | 16017360 | 16017498 |
| chr_3 | g2209 | g2209.t1 | cds | g2209.t1.CDS2 | 16017360 | 16017498 |
| chr_3 | g2209 | g2209.t1 | exon | g2209.t1.exon3 | 16017633 | 16018008 |
| chr_3 | g2209 | g2209.t1 | cds | g2209.t1.CDS3 | 16017633 | 16018008 |
| chr_3 | g2209 | g2209.t1 | exon | g2209.t1.exon4 | 16018081 | 16018233 |
| chr_3 | g2209 | g2209.t1 | cds | g2209.t1.CDS4 | 16018081 | 16018233 |
| chr_3 | g2209 | g2209.t1 | exon | g2209.t1.exon5 | 16018637 | 16019894 |
| chr_3 | g2209 | g2209.t1 | cds | g2209.t1.CDS5 | 16018637 | 16019894 |
| chr_3 | g2209 | g2209.t1 | TTS | g2209.t1 | 16020530 | 16020530 |
Sequences
>g2209.t1 Gene=g2209 Length=1980
ATGACTGGTCTCTTAAAGTGTTCTACATTATTAGCAAGAAACACACAGAACCTTCTAAAG
ACACTTTCGTTTACATCGTCAAGAAATCTTCATTTTACGGTCGGAAACAATAATTCCAAA
GCAAATCCAAATGCCATATCAAATGCTTATCAAGTAGTTGATCATGAATTTGACGCTGTT
GTCGTCGGTGCAGGCGGTGCTGGTCTTCGAGCTGCTTTTGGTCTCGTTGCCGAAGGTTTC
AAAACAGCTGTTGTGACAAAATTATTCCCCACACGATCACATACAGTTGCTGCACAAGGA
GGAATCAATGCAGCTCTCGGGAATATGGAACCCGATGACTGGAAATGGCACATGTATGAT
ACAGTTAAGGGATCAGATTGGTTAGGCGATCAAGATGCAATCAATTACATGACTCGCGAA
GCACCAAAAGCTGTTATTGAACTTGAAAATTATGGAATGCCATTCTCACGTACACCAGAT
GGAAAAATTTATCAACGTGCCTTTGGTGGTCAAAGTTATAACTATGGAAAAGGTGGTCAG
GCACATCGATGCTGTTGCGTTGCTGACAGAACCGGTCACTCGCTTCTACACACTCTCTAT
GGTCAATCCCTTAGCTACAATTGCAACTATTTTATCGAATATTTTGCTATGGATTTAATT
ATGCAAAATGGTGAATGCCATGGCGTTATTGCCTTAAACTTAGAAGATGGAACAATTCAT
CGTTTCCGAGCAAAGAATACAGTACTCGCAACTGGCGGTTATGGACGTGCATATTTCTCT
TGCACATCAGCACATACGTGTACTGGTGATGGCACTGCTATGGTGGCTCGTGCTGGTCTT
CCTTCAGAAGACTTGGAATTTGTGCAATTTCATCCAACCGGTATCTATGGTGCTGGTTGT
TTGATTACAGAAGGTTGTCGCGGTGAAGGAGGCTATTTAATTAATTCACAAGGAGAACGT
TTTATGGAACGTTATGCTCCAGTTGCTAAGGATTTGGCCTCACGTGATGTTGTCTCACGT
TCAATGACAATTGAAATTCGTGAGGGAAGAGGCTGTGGTCCCGAGAAAGACCACGTTTAC
TTGCAATTACACCATTTGCCCCCAGAACAATTGGCTCAACGTTTGCCGGGTATCTCGGAA
ACTGCAATGATTTTTGCTGGTGTTGATGTTACACGTGAGCCAATTCCTGTTCTCCCTACA
GTTCACTATAACATGGGCGGTGTGCCAACAAATTACAAGGGTCAAGTGCTGACTATCGAT
AAGAAAGGAGATGATGTTATTGTACCTGGACTTTATGCTTGTGGAGAAGCTGCATGCTCT
TCTGTACATGGTGCTAATCGTTTAGGTGCAAATTCACTTTTAGATTTAGTTGTATTTGGA
CGTGCTTGTGCAAAGACAATCGCTGAAGAGAATAAACCAGGCGAGAAACTTCCCAATCTC
CCTGATAATGCTGGTGAAGAATCCGTTGCTAATTTAGATTGGGTACGAAATGCAAGTGGT
GCAGTACCAACTGCTGATTTGCGTTTGAAAATGCAGAAAACTATGCAAAATCACGCTGCT
GTGTTCCGTGAAGCTAAAACACTCCAAGAGGGTGTACAAAAAATGTCAGGCATCTATAAA
CAAATCAAAGACGTAAAAGTGTCTGATCGCTCACTTATTTGGAATTCAGATTTAATTGAA
ACATTAGAATTGCAAAATCTTTTGCTTAATGCTAACATGACTATGGTTGCTGCTGAAAAT
CGCAAAGAATCACGCGGTGCCCATGCTCGTGAAGATTTTAAAGATCGCATTGATGAATTT
GATTATAGTAAGCCAATCGAGGGTCAACAAAAGAAACCAATCACAGAACACTGGAGAAAG
CACACTCTCACGTGGATCAATAAAGACACTGGTGATGTTACTATCGATTACAGACCTGTT
ATTGATACAACACTCGATAACGAATGTAAAACAGTCCCACCAGCCATTCGTTCATACTAA
>g2209.t1 Gene=g2209 Length=659
MTGLLKCSTLLARNTQNLLKTLSFTSSRNLHFTVGNNNSKANPNAISNAYQVVDHEFDAV
VVGAGGAGLRAAFGLVAEGFKTAVVTKLFPTRSHTVAAQGGINAALGNMEPDDWKWHMYD
TVKGSDWLGDQDAINYMTREAPKAVIELENYGMPFSRTPDGKIYQRAFGGQSYNYGKGGQ
AHRCCCVADRTGHSLLHTLYGQSLSYNCNYFIEYFAMDLIMQNGECHGVIALNLEDGTIH
RFRAKNTVLATGGYGRAYFSCTSAHTCTGDGTAMVARAGLPSEDLEFVQFHPTGIYGAGC
LITEGCRGEGGYLINSQGERFMERYAPVAKDLASRDVVSRSMTIEIREGRGCGPEKDHVY
LQLHHLPPEQLAQRLPGISETAMIFAGVDVTREPIPVLPTVHYNMGGVPTNYKGQVLTID
KKGDDVIVPGLYACGEAACSSVHGANRLGANSLLDLVVFGRACAKTIAEENKPGEKLPNL
PDNAGEESVANLDWVRNASGAVPTADLRLKMQKTMQNHAAVFREAKTLQEGVQKMSGIYK
QIKDVKVSDRSLIWNSDLIETLELQNLLLNANMTMVAAENRKESRGAHAREDFKDRIDEF
DYSKPIEGQQKKPITEHWRKHTLTWINKDTGDVTIDYRPVIDTTLDNECKTVPPAIRSY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2209.t1 | Gene3D | G3DSA:3.50.50.60 | - | 58 | 464 | 2.4E-176 |
| 9 | g2209.t1 | Gene3D | G3DSA:3.90.700.10 | Flavocytochrome C3; Chain A | 295 | 398 | 2.4E-176 |
| 10 | g2209.t1 | Gene3D | G3DSA:1.20.58.100 | - | 481 | 595 | 6.0E-41 |
| 12 | g2209.t1 | Gene3D | G3DSA:4.10.80.40 | succinate dehydrogenase protein domain | 596 | 659 | 2.1E-34 |
| 3 | g2209.t1 | PANTHER | PTHR11632 | SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT | 47 | 659 | 0.0 |
| 4 | g2209.t1 | PANTHER | PTHR11632:SF51 | SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL | 47 | 659 | 0.0 |
| 15 | g2209.t1 | PIRSF | PIRSF000171 | SDHA_APRA_LASPO | 47 | 624 | 1.5E-38 |
| 2 | g2209.t1 | Pfam | PF00890 | FAD binding domain | 58 | 453 | 7.3E-129 |
| 1 | g2209.t1 | Pfam | PF02910 | Fumarate reductase flavoprotein C-term | 508 | 659 | 8.9E-43 |
| 8 | g2209.t1 | ProSitePatterns | PS00504 | Fumarate reductase / succinate dehydrogenase FAD-binding site. | 92 | 101 | - |
| 7 | g2209.t1 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 49 | 483 | 2.72E-80 |
| 5 | g2209.t1 | SUPERFAMILY | SSF56425 | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 285 | 403 | 2.54E-42 |
| 6 | g2209.t1 | SUPERFAMILY | SSF46977 | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 500 | 659 | 3.14E-45 |
| 13 | g2209.t1 | TIGRFAM | TIGR01816 | sdhA_forward: succinate dehydrogenase, flavoprotein subunit | 55 | 659 | 8.4E-302 |
| 14 | g2209.t1 | TIGRFAM | TIGR01812 | sdhA_frdA_Gneg: succinate dehydrogenase or fumarate reductase, flavoprotein subunit | 58 | 643 | 1.9E-229 |
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 transcript has been annotated with K00234 (succinate dehydrogenase (ubiquinone) flavoprotein subunit)
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.
