Gene loci information

Transcript annotation

  • This transcript has been annotated as Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial.

Parent gene

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.t5 TSS g2209.t5 16017010 16017010
chr_3 g2209 g2209.t5 isoform g2209.t5 16017065 16019894
chr_3 g2209 g2209.t5 exon g2209.t5.exon1 16017065 16017122
chr_3 g2209 g2209.t5 exon g2209.t5.exon2 16017360 16017498
chr_3 g2209 g2209.t5 exon g2209.t5.exon3 16017633 16018008
chr_3 g2209 g2209.t5 cds g2209.t5.CDS1 16017764 16018008
chr_3 g2209 g2209.t5 exon g2209.t5.exon4 16018081 16018233
chr_3 g2209 g2209.t5 cds g2209.t5.CDS2 16018081 16018233
chr_3 g2209 g2209.t5 exon g2209.t5.exon5 16018637 16019894
chr_3 g2209 g2209.t5 cds g2209.t5.CDS3 16018637 16019894
chr_3 g2209 g2209.t5 TTS g2209.t5 16020530 16020530

Sequences

>g2209.t5 Gene=g2209 Length=1984
ATGACTGGTCTCTTAAAGTGTTCTACATTATTAGCAAGAAACACACAGAACCTTGTAACT
AAAGACACTTTCGTTTACATCGTCAAGAAATCTTCATTTTACGGTCGGAAACAATAATTC
CAAAGCAAATCCAAATGCCATATCAAATGCTTATCAAGTAGTTGATCATGAATTTGACGC
TGTTGTCGTCGGTGCAGGCGGTGCTGGTCTTCGAGCTGCTTTTGGTCTCGTTGCCGAAGG
TTTCAAAACAGCTGTTGTGACAAAATTATTCCCCACACGATCACATACAGTTGCTGCACA
AGGAGGAATCAATGCAGCTCTCGGGAATATGGAACCCGATGACTGGAAATGGCACATGTA
TGATACAGTTAAGGGATCAGATTGGTTAGGCGATCAAGATGCAATCAATTACATGACTCG
CGAAGCACCAAAAGCTGTTATTGAACTTGAAAATTATGGAATGCCATTCTCACGTACACC
AGATGGAAAAATTTATCAACGTGCCTTTGGTGGTCAAAGTTATAACTATGGAAAAGGTGG
TCAGGCACATCGATGCTGTTGCGTTGCTGACAGAACCGGTCACTCGCTTCTACACACTCT
CTATGGTCAATCCCTTAGCTACAATTGCAACTATTTTATCGAATATTTTGCTATGGATTT
AATTATGCAAAATGGTGAATGCCATGGCGTTATTGCCTTAAACTTAGAAGATGGAACAAT
TCATCGTTTCCGAGCAAAGAATACAGTACTCGCAACTGGCGGTTATGGACGTGCATATTT
CTCTTGCACATCAGCACATACGTGTACTGGTGATGGCACTGCTATGGTGGCTCGTGCTGG
TCTTCCTTCAGAAGACTTGGAATTTGTGCAATTTCATCCAACCGGTATCTATGGTGCTGG
TTGTTTGATTACAGAAGGTTGTCGCGGTGAAGGAGGCTATTTAATTAATTCACAAGGAGA
ACGTTTTATGGAACGTTATGCTCCAGTTGCTAAGGATTTGGCCTCACGTGATGTTGTCTC
ACGTTCAATGACAATTGAAATTCGTGAGGGAAGAGGCTGTGGTCCCGAGAAAGACCACGT
TTACTTGCAATTACACCATTTGCCCCCAGAACAATTGGCTCAACGTTTGCCGGGTATCTC
GGAAACTGCAATGATTTTTGCTGGTGTTGATGTTACACGTGAGCCAATTCCTGTTCTCCC
TACAGTTCACTATAACATGGGCGGTGTGCCAACAAATTACAAGGGTCAAGTGCTGACTAT
CGATAAGAAAGGAGATGATGTTATTGTACCTGGACTTTATGCTTGTGGAGAAGCTGCATG
CTCTTCTGTACATGGTGCTAATCGTTTAGGTGCAAATTCACTTTTAGATTTAGTTGTATT
TGGACGTGCTTGTGCAAAGACAATCGCTGAAGAGAATAAACCAGGCGAGAAACTTCCCAA
TCTCCCTGATAATGCTGGTGAAGAATCCGTTGCTAATTTAGATTGGGTACGAAATGCAAG
TGGTGCAGTACCAACTGCTGATTTGCGTTTGAAAATGCAGAAAACTATGCAAAATCACGC
TGCTGTGTTCCGTGAAGCTAAAACACTCCAAGAGGGTGTACAAAAAATGTCAGGCATCTA
TAAACAAATCAAAGACGTAAAAGTGTCTGATCGCTCACTTATTTGGAATTCAGATTTAAT
TGAAACATTAGAATTGCAAAATCTTTTGCTTAATGCTAACATGACTATGGTTGCTGCTGA
AAATCGCAAAGAATCACGCGGTGCCCATGCTCGTGAAGATTTTAAAGATCGCATTGATGA
ATTTGATTATAGTAAGCCAATCGAGGGTCAACAAAAGAAACCAATCACAGAACACTGGAG
AAAGCACACTCTCACGTGGATCAATAAAGACACTGGTGATGTTACTATCGATTACAGACC
TGTTATTGATACAACACTCGATAACGAATGTAAAACAGTCCCACCAGCCATTCGTTCATA
CTAA

>g2209.t5 Gene=g2209 Length=551
MEPDDWKWHMYDTVKGSDWLGDQDAINYMTREAPKAVIELENYGMPFSRTPDGKIYQRAF
GGQSYNYGKGGQAHRCCCVADRTGHSLLHTLYGQSLSYNCNYFIEYFAMDLIMQNGECHG
VIALNLEDGTIHRFRAKNTVLATGGYGRAYFSCTSAHTCTGDGTAMVARAGLPSEDLEFV
QFHPTGIYGAGCLITEGCRGEGGYLINSQGERFMERYAPVAKDLASRDVVSRSMTIEIRE
GRGCGPEKDHVYLQLHHLPPEQLAQRLPGISETAMIFAGVDVTREPIPVLPTVHYNMGGV
PTNYKGQVLTIDKKGDDVIVPGLYACGEAACSSVHGANRLGANSLLDLVVFGRACAKTIA
EENKPGEKLPNLPDNAGEESVANLDWVRNASGAVPTADLRLKMQKTMQNHAAVFREAKTL
QEGVQKMSGIYKQIKDVKVSDRSLIWNSDLIETLELQNLLLNANMTMVAAENRKESRGAH
AREDFKDRIDEFDYSKPIEGQQKKPITEHWRKHTLTWINKDTGDVTIDYRPVIDTTLDNE
CKTVPPAIRSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g2209.t5 Gene3D G3DSA:3.50.50.60 - 2 356 0
8 g2209.t5 Gene3D G3DSA:3.90.700.10 Flavocytochrome C3; Chain A 187 290 0
9 g2209.t5 Gene3D G3DSA:1.20.58.100 - 373 487 0
11 g2209.t5 Gene3D G3DSA:4.10.80.40 succinate dehydrogenase protein domain 488 551 0
3 g2209.t5 PANTHER PTHR11632 SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT 1 551 0
4 g2209.t5 PANTHER PTHR11632:SF51 SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL 1 551 0
14 g2209.t5 PIRSF PIRSF000171 SDHA_APRA_LASPO 14 516 0
2 g2209.t5 Pfam PF00890 FAD binding domain 3 345 0
1 g2209.t5 Pfam PF02910 Fumarate reductase flavoprotein C-term 400 551 0
7 g2209.t5 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain 4 375 0
5 g2209.t5 SUPERFAMILY SSF56425 Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 177 295 0
6 g2209.t5 SUPERFAMILY SSF46977 Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain 392 551 0
12 g2209.t5 TIGRFAM TIGR01816 sdhA_forward: succinate dehydrogenase, flavoprotein subunit 1 551 0
13 g2209.t5 TIGRFAM TIGR01812 sdhA_frdA_Gneg: succinate dehydrogenase or fumarate reductase, flavoprotein subunit 3 536 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: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

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.

Raw TPM values