Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Succinate dehydrogenase cytochrome b560 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_4 g17494 g17494.t3 TSS g17494.t3 13669597 13669597
chr_4 g17494 g17494.t3 isoform g17494.t3 13669604 13676923
chr_4 g17494 g17494.t3 exon g17494.t3.exon1 13669604 13669748
chr_4 g17494 g17494.t3 exon g17494.t3.exon2 13676247 13676325
chr_4 g17494 g17494.t3 cds g17494.t3.CDS1 13676306 13676325
chr_4 g17494 g17494.t3 exon g17494.t3.exon3 13676431 13676923
chr_4 g17494 g17494.t3 cds g17494.t3.CDS2 13676431 13676923
chr_4 g17494 g17494.t3 TTS g17494.t3 13677002 13677002

Sequences

>g17494.t3 Gene=g17494 Length=717
AGTAAAAATTACATAAAATTGCGTATTTCAAAATAAATAATTTTTTATTTCGAGATTCTT
AATTATGTTTACAGTGTTTACTAAATAAAAAATACTTTAATAAGGAACTTTAATACTATT
ACAAATCATTAAATGATTAATAGTGTCTCAATTCAAACAGTCTACGAAAAATTTCATTTT
AACTCTAATAAGGCAAAAATAAGGATGGCATTGTGTTTGGCAAGAAATTTTTGCTACCGC
GCAATAAACTTCAATCCATCGCAATTAAATTCTTCTCGTTATGTATCATTGAAGGTAGTT
AAAAATATACCTCCACCACAAAATGAACGATATGATGAAAGAGGAGCAAGATTCAAGCGT
CCAATATCACCACATCTTTCCATTTACCAGCCACAAATAACATCTGTGCTTTCTATTAGT
CATCGTATGACTGGAGTTGCTTTATCTGCTTATATAATTGGCGCTGGAATCACTGGCCTC
ATGGGAGGAGATTCTTCAATTATTTCTACAATTGAAGGCTGGCAACTTGGAGCAGCTTCA
CTTACAGCATTAAAATTCAGTATTGCTTTTCCATTTGTTTATCATTATTTCAATGGCATT
CGTCATTTATTATGGGATGTTGGATTTTTTTTAAATGTTAAAGAAATTTATGTTACTGGC
TATGCAGTGCTTTTTGCTACATTTATTGCAACTATAGCACTTACATTTTATTTTTAA

>g17494.t3 Gene=g17494 Length=170
MALCLARNFCYRAINFNPSQLNSSRYVSLKVVKNIPPPQNERYDERGARFKRPISPHLSI
YQPQITSVLSISHRMTGVALSAYIIGAGITGLMGGDSSIISTIEGWQLGAASLTALKFSI
AFPFVYHYFNGIRHLLWDVGFFLNVKEIYVTGYAVLFATFIATIALTFYF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g17494.t3 CDD cd03499 SQR_TypeC_SdhC 52 168 1.23806E-33
5 g17494.t3 Gene3D G3DSA:1.20.1300.10 Fumarate reductase respiratory complex transmembrane subunits 37 170 9.9E-46
2 g17494.t3 PANTHER PTHR10978 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT 41 168 2.6E-37
3 g17494.t3 PANTHER PTHR10978:SF5 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT, MITOCHONDRIAL 41 168 2.6E-37
1 g17494.t3 Pfam PF01127 Succinate dehydrogenase/Fumarate reductase transmembrane subunit 50 166 1.9E-23
9 g17494.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 74 -
10 g17494.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 75 94 -
7 g17494.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 95 105 -
12 g17494.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 106 128 -
8 g17494.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 129 147 -
11 g17494.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 148 169 -
6 g17494.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 170 170 -
17 g17494.t3 ProSitePatterns PS01000 Succinate dehydrogenase cytochrome b subunit signature 1. 52 76 -
18 g17494.t3 ProSitePatterns PS01001 Succinate dehydrogenase cytochrome b subunit signature 2. 127 140 -
4 g17494.t3 SUPERFAMILY SSF81343 Fumarate reductase respiratory complex transmembrane subunits 48 169 5.23E-27
19 g17494.t3 TIGRFAM TIGR02970 succ_dehyd_cytB: succinate dehydrogenase, cytochrome b556 subunit 51 168 5.3E-24
16 g17494.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -
14 g17494.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 110 129 -
15 g17494.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 150 169 -

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