Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Succinate dehydrogenase cytochrome B 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 g703 g703.t1 TTS g703.t1 5437966 5437966
chr_3 g703 g703.t1 isoform g703.t1 5438031 5438650
chr_3 g703 g703.t1 exon g703.t1.exon1 5438031 5438517
chr_3 g703 g703.t1 cds g703.t1.CDS1 5438031 5438517
chr_3 g703 g703.t1 exon g703.t1.exon2 5438631 5438650
chr_3 g703 g703.t1 cds g703.t1.CDS2 5438631 5438650
chr_3 g703 g703.t1 TSS g703.t1 5438741 5438741

Sequences

>g703.t1 Gene=g703 Length=507
ATGGCATTGTGTTTGGCAAGAAATTTTTGCAACCGTGCAACAATCTTCAATCCAGCTCAA
TTAAGTTCTGCTCGTTATGTATCGATCAAAGTAGTTCCAGCAACTCAACCAGCTGTAGAG
GGACATGATGCACGAAACGCTAGATTTAAGCGTCCTCAATCACCACATCTTACCATTTAT
AAGCCTCAATTGACATCTATGCTTTCAATCACTCATCGTGGAACAGGCATTTTATTGTCA
TCTTATGTGATTGCAGCTGGAATTGCCGGTATTTCAGGAGACTTTTCCGTTGTTTCATCA
ATTGAAGCTTTGCAACTTGGCGCCGCATCGTTAGCAGCACTTAAATTCAGCATTGCTTTT
CCATTTTCTTATCATCTTGTCAATGGTATTCGTCATTTGTTTTGGGATATGGGAAAATTC
TTGAGTATTAAAGAAGTCTATACTACTGGATATGCTATGCTTTTTGCATCAATTGTTCTT
TCTTTGGCACTTACGTTTTTGTTTTAA

>g703.t1 Gene=g703 Length=168
MALCLARNFCNRATIFNPAQLSSARYVSIKVVPATQPAVEGHDARNARFKRPQSPHLTIY
KPQLTSMLSITHRGTGILLSSYVIAAGIAGISGDFSVVSSIEALQLGAASLAALKFSIAF
PFSYHLVNGIRHLFWDMGKFLSIKEVYTTGYAMLFASIVLSLALTFLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g703.t1 CDD cd03499 SQR_TypeC_SdhC 51 166 2.45859E-35
5 g703.t1 Gene3D G3DSA:1.20.1300.10 Fumarate reductase respiratory complex transmembrane subunits 34 167 1.1E-45
2 g703.t1 PANTHER PTHR10978 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT 31 166 9.3E-40
3 g703.t1 PANTHER PTHR10978:SF5 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT, MITOCHONDRIAL 31 166 9.3E-40
1 g703.t1 Pfam PF01127 Succinate dehydrogenase/Fumarate reductase transmembrane subunit 49 164 1.1E-23
6 g703.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 76 -
10 g703.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 77 98 -
8 g703.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 99 103 -
11 g703.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 127 -
7 g703.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 128 147 -
12 g703.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 148 167 -
9 g703.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 168 168 -
17 g703.t1 ProSitePatterns PS01001 Succinate dehydrogenase cytochrome b subunit signature 2. 125 138 -
4 g703.t1 SUPERFAMILY SSF81343 Fumarate reductase respiratory complex transmembrane subunits 45 166 1.46E-28
18 g703.t1 TIGRFAM TIGR02970 succ_dehyd_cytB: succinate dehydrogenase, cytochrome b556 subunit 50 166 1.3E-23
14 g703.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 76 98 -
16 g703.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 108 130 -
15 g703.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 150 167 -

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:0016020 membrane CC
GO:0009055 electron transfer activity MF
GO:0006099 tricarboxylic acid cycle BP
GO:0045281 succinate dehydrogenase complex CC
GO:0000104 succinate dehydrogenase 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