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.t3 TSS g2209.t3 16017010 16017010
chr_3 g2209 g2209.t3 isoform g2209.t3 16017065 16018655
chr_3 g2209 g2209.t3 exon g2209.t3.exon1 16017065 16017118
chr_3 g2209 g2209.t3 cds g2209.t3.CDS1 16017065 16017118
chr_3 g2209 g2209.t3 exon g2209.t3.exon2 16017360 16017498
chr_3 g2209 g2209.t3 cds g2209.t3.CDS2 16017360 16017498
chr_3 g2209 g2209.t3 exon g2209.t3.exon3 16017651 16018008
chr_3 g2209 g2209.t3 cds g2209.t3.CDS3 16017651 16018008
chr_3 g2209 g2209.t3 exon g2209.t3.exon4 16018081 16018233
chr_3 g2209 g2209.t3 cds g2209.t3.CDS4 16018081 16018233
chr_3 g2209 g2209.t3 exon g2209.t3.exon5 16018637 16018655
chr_3 g2209 g2209.t3 cds g2209.t3.CDS5 16018637 16018655
chr_3 g2209 g2209.t3 TTS g2209.t3 NA NA

Sequences

>g2209.t3 Gene=g2209 Length=723
ATGACTGGTCTCTTAAAGTGTTCTACATTATTAGCAAGAAACACACAGAACCTTCTAAAG
ACACTTTCGTTTACATCGTCAAGAAATCTTCATTTTACGGTCGGAAACAATAATTCCAAA
GCAAATCCAAATGCCATATCAAATGCTTATCAAGTAGTTGATCATGAATTTGACGCTGTT
GTCGTCGGTGCAGCTGCTTTTGGTCTCGTTGCCGAAGGTTTCAAAACAGCTGTTGTGACA
AAATTATTCCCCACACGATCACATACAGTTGCTGCACAAGGAGGAATCAATGCAGCTCTC
GGGAATATGGAACCCGATGACTGGAAATGGCACATGTATGATACAGTTAAGGGATCAGAT
TGGTTAGGCGATCAAGATGCAATCAATTACATGACTCGCGAAGCACCAAAAGCTGTTATT
GAACTTGAAAATTATGGAATGCCATTCTCACGTACACCAGATGGAAAAATTTATCAACGT
GCCTTTGGTGGTCAAAGTTATAACTATGGAAAAGGTGGTCAGGCACATCGATGCTGTTGC
GTTGCTGACAGAACCGGTCACTCGCTTCTACACACTCTCTATGGTCAATCCCTTAGCTAC
AATTGCAACTATTTTATCGAATATTTTGCTATGGATTTAATTATGCAAAATGGTGAATGC
CATGGCGTTATTGCCTTAAACTTAGAAGATGGAACAATTCATCGTTTCCGAGCAAAGAAT
ACA

>g2209.t3 Gene=g2209 Length=241
MTGLLKCSTLLARNTQNLLKTLSFTSSRNLHFTVGNNNSKANPNAISNAYQVVDHEFDAV
VVGAAAFGLVAEGFKTAVVTKLFPTRSHTVAAQGGINAALGNMEPDDWKWHMYDTVKGSD
WLGDQDAINYMTREAPKAVIELENYGMPFSRTPDGKIYQRAFGGQSYNYGKGGQAHRCCC
VADRTGHSLLHTLYGQSLSYNCNYFIEYFAMDLIMQNGECHGVIALNLEDGTIHRFRAKN
T

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2209.t3 Gene3D G3DSA:3.50.50.60 - 39 241 7.7E-76
2 g2209.t3 PANTHER PTHR11632 SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT 47 241 2.4E-109
3 g2209.t3 PANTHER PTHR11632:SF51 SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL 47 241 2.4E-109
1 g2209.t3 Pfam PF00890 FAD binding domain 64 240 2.2E-46
5 g2209.t3 ProSitePatterns PS00504 Fumarate reductase / succinate dehydrogenase FAD-binding site. 86 95 -
4 g2209.t3 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain 49 240 2.97E-39

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. There were no conditions that were differentially expressed