Gene loci information

Transcript annotation

  • This transcript has been annotated as Succinate dehydrogenase [ubiquinone] iron-sulfur 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_2 g7717 g7717.t5 TTS g7717.t5 25443895 25443895
chr_2 g7717 g7717.t5 isoform g7717.t5 25443941 25445177
chr_2 g7717 g7717.t5 exon g7717.t5.exon1 25443941 25444336
chr_2 g7717 g7717.t5 cds g7717.t5.CDS1 25443941 25444336
chr_2 g7717 g7717.t5 exon g7717.t5.exon2 25444397 25445177
chr_2 g7717 g7717.t5 cds g7717.t5.CDS2 25444397 25444411
chr_2 g7717 g7717.t5 TSS g7717.t5 25445263 25445263

Sequences

>g7717.t5 Gene=g7717 Length=1177
ATGGCACTTGCAAATGATTTGAGAATAATTTTGGCAACAAGAGGAGCATTAAGTCATGTA
AGTTTAAGTAAAACATGAGTTTAAATAGTATAAAAACTAGTTTCTTCATTTGCTATTATG
ATTGAATAACTTTTTCTCAATCTATTTTGGGGCTAATTAGAATGTGATGTTAATTGAAGT
AAAGTTTGTGTACAGATAATGATTGATAAAGAAGATAAGAATTTAATACAGATAACGGAC
AAGTAAAAAGCTTTTAGTTAATTTTCTCTTGATGAATACAGGAATTACTTACATAAAACT
TCTAGAAAATTTACATTGTTACATTAGAAAAATAAAGAATATATTTTTTGTTTCAAAAAT
ATTTATAGCTCCGCAGCATTCATTCATCGTCAGCTGCAAGTGCTGCTCAAAAAATCAAAA
CTTTTGAGATCTATCGCTATAATCCAGAAAAGCCTGATGAGAAGCCTCGTATGCAATCGT
ATAAAGTTGATCTCAACACTTGTGGTCCAATGGTTCTTGATGCTTTAATTAAAATTAAAA
ATGAAATGGATCCAACTCTCACTTTCCGTCGTTCATGTCGCGAGGGAATTTGTGGTTCAT
GTGCAATGAACATTGGTGGAACAAATACTTTGGCTTGCATTAGTAAAATTGATGCTTCAA
ATTTGGATAGACCAGTAAAGATCTATCCATTGCCCCATATGTATGTCGTTAAAGACCTTG
TTCCTGATTTTACCAACTTTTACAATCAATATCGTTCTATTCAACCATGGCTTCAACGCA
AAGGAATGAAAAGACTGAGGAAAAGGGTAAAGCACAATATCTTCAATCAGTTGATGATCG
ATCAAAACTTGATGGCCTCTATGAATGCATTTTATGTGCATGTTGTTCAACATCGTGTCC
TAGCTATTGGTGGAATTCAGAAAAATATTTGGGACCAGCTGTACTTATGCAAGCATATAG
ATGGATTATTGATTCACGTGATGAATCGACAAAGGCTCGTTTGGATAAATTGAGAGATCC
ATTCAGTGTATATCGTTGTCATACAATTATGAATTGCTCTCGTACATGTCCAAAAGGACT
TAATCCTGGAAAAGCAATTGCAGAAATCAAAAAGCTTCTCGGTGGTCTGGCGACAAAAGA
TGCTCCTGGCTTAGAAACAGCAAAGTTACACAAGTAA

>g7717.t5 Gene=g7717 Length=136
MASTQRNEKTEEKGKAQYLQSVDDRSKLDGLYECILCACCSTSCPSYWWNSEKYLGPAVL
MQAYRWIIDSRDESTKARLDKLRDPFSVYRCHTIMNCSRTCPKGLNPGKAIAEIKKLLGG
LATKDAPGLETAKLHK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7717.t5 Gene3D G3DSA:1.10.1060.10 - 2 127 4.4E-56
2 g7717.t5 PANTHER PTHR11921 SUCCINATE DEHYDROGENASE IRON-SULFUR PROTEIN 8 122 7.5E-59
3 g7717.t5 PANTHER PTHR11921:SF29 SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR SUBUNIT, MITOCHONDRIAL 8 122 7.5E-59
1 g7717.t5 Pfam PF13534 4Fe-4S dicluster domain 33 106 6.0E-11
5 g7717.t5 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature. 34 45 -
8 g7717.t5 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. 24 54 7.55
4 g7717.t5 SUPERFAMILY SSF46548 alpha-helical ferredoxin 14 117 8.37E-34
7 g7717.t5 TIGRFAM TIGR00384 dhsB: succinate dehydrogenase and fumarate reductase iron-sulfur protein 9 115 2.0E-38

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:0006099 tricarboxylic acid cycle BP
GO:0055114 NA NA
GO:0051536 iron-sulfur cluster binding MF
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.

Raw TPM values