Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Succinate dehydrogenase [ubiquinone] cytochrome b small 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 g2694 g2694.t1 TTS g2694.t1 19731095 19731095
chr_3 g2694 g2694.t1 isoform g2694.t1 19731243 19731952
chr_3 g2694 g2694.t1 exon g2694.t1.exon1 19731243 19731614
chr_3 g2694 g2694.t1 cds g2694.t1.CDS1 19731243 19731614
chr_3 g2694 g2694.t1 exon g2694.t1.exon2 19731691 19731761
chr_3 g2694 g2694.t1 cds g2694.t1.CDS2 19731691 19731761
chr_3 g2694 g2694.t1 exon g2694.t1.exon3 19731907 19731952
chr_3 g2694 g2694.t1 cds g2694.t1.CDS3 19731907 19731952
chr_3 g2694 g2694.t1 TSS g2694.t1 19732010 19732010

Sequences

>g2694.t1 Gene=g2694 Length=489
ATGGCATTATCTATGCTTCTTCGTTCTTCATCAAGACTTTCACCAGTCTTAATGAACGCT
TCACGAATTAGTTGTGCGCCAGTAACTCCGATACTTGCAAATAAAATTGCCATCAATAAT
TCTAGACAAATTTCTGTAAGTCCTATTCGTCAGTCTGCAACGGGTAATCATGTAGCATTA
TGGCAAGCAGAAAGAGCACTATCAGTTGGGCTTTTGGGCATTGTTCCAGTTTCATTTTTG
ATTGAATCACAAGCTTCTGAATATCTTCTTTCACTCGCTCTCGTTATGCATTTTCATTGG
GGTTTGGAAGCACTCGTTACCGATTATGTTCGTGAAGAACTTTTCGGCTCGTTACTTCCA
AAAGTTTCACATGTTCTCCTTGCTCTCATTTCGGCAGCTACATTAGCAGGACTTTTCATG
ATGGCTTATAAAGATCAAGGACTCGCAAAAACAACTCGCAAGATTTGGGCTATTCAACCA
GCAAATTAA

>g2694.t1 Gene=g2694 Length=162
MALSMLLRSSSRLSPVLMNASRISCAPVTPILANKIAINNSRQISVSPIRQSATGNHVAL
WQAERALSVGLLGIVPVSFLIESQASEYLLSLALVMHFHWGLEALVTDYVREELFGSLLP
KVSHVLLALISAATLAGLFMMAYKDQGLAKTTRKIWAIQPAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2694.t1 Gene3D G3DSA:1.20.1300.10 Fumarate reductase respiratory complex transmembrane subunits 31 158 9.4E-36
2 g2694.t1 PANTHER PTHR13337:SF2 SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL 1 157 9.5E-31
3 g2694.t1 PANTHER PTHR13337 SUCCINATE DEHYDROGENASE 1 157 9.5E-31
1 g2694.t1 Pfam PF05328 CybS, succinate dehydrogenase cytochrome B small subunit 45 157 2.3E-30
8 g2694.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 87 -
11 g2694.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 110 -
9 g2694.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 121 -
10 g2694.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 143 -
7 g2694.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 144 162 -
5 g2694.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 20 -
4 g2694.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 124 143 -

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:0016020 membrane CC
GO:0005740 mitochondrial envelope CC
GO:0016021 integral component of membrane CC

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