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.t90 TTS g2694.t90 19731095 19731095
chr_3 g2694 g2694.t90 isoform g2694.t90 19731243 19731952
chr_3 g2694 g2694.t90 exon g2694.t90.exon1 19731243 19731614
chr_3 g2694 g2694.t90 cds g2694.t90.CDS1 19731243 19731614
chr_3 g2694 g2694.t90 exon g2694.t90.exon2 19731691 19731761
chr_3 g2694 g2694.t90 cds g2694.t90.CDS2 19731691 19731761
chr_3 g2694 g2694.t90 exon g2694.t90.exon3 19731931 19731952
chr_3 g2694 g2694.t90 cds g2694.t90.CDS3 19731931 19731952
chr_3 g2694 g2694.t90 TSS g2694.t90 19732010 19732010

Sequences

>g2694.t90 Gene=g2694 Length=465
ATGGCATTATCTATGCTTCTTCTCTTAATGAACGCTTCACGAATTAGTTGTGCGCCAGTA
ACTCCGATACTTGCAAATAAAATTGCCATCAATAATTCTAGACAAATTTCTGTAAGTCCT
ATTCGTCAGTCTGCAACGGGTAATCATGTAGCATTATGGCAAGCAGAAAGAGCACTATCA
GTTGGGCTTTTGGGCATTGTTCCAGTTTCATTTTTGATTGAATCACAAGCTTCTGAATAT
CTTCTTTCACTCGCTCTCGTTATGCATTTTCATTGGGGTTTGGAAGCACTCGTTACCGAT
TATGTTCGTGAAGAACTTTTCGGCTCGTTACTTCCAAAAGTTTCACATGTTCTCCTTGCT
CTCATTTCGGCAGCTACATTAGCAGGACTTTTCATGATGGCTTATAAAGATCAAGGACTC
GCAAAAACAACTCGCAAGATTTGGGCTATTCAACCAGCAAATTAA

>g2694.t90 Gene=g2694 Length=154
MALSMLLLLMNASRISCAPVTPILANKIAINNSRQISVSPIRQSATGNHVALWQAERALS
VGLLGIVPVSFLIESQASEYLLSLALVMHFHWGLEALVTDYVREELFGSLLPKVSHVLLA
LISAATLAGLFMMAYKDQGLAKTTRKIWAIQPAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2694.t90 Gene3D G3DSA:1.20.1300.10 Fumarate reductase respiratory complex transmembrane subunits 19 150 6.5E-36
2 g2694.t90 PANTHER PTHR13337:SF2 SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL 26 149 6.0E-30
3 g2694.t90 PANTHER PTHR13337 SUCCINATE DEHYDROGENASE 26 149 6.0E-30
1 g2694.t90 Pfam PF05328 CybS, succinate dehydrogenase cytochrome B small subunit 37 149 1.9E-30
11 g2694.t90 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
12 g2694.t90 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
13 g2694.t90 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 9 -
17 g2694.t90 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 10 17 -
9 g2694.t90 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 56 -
14 g2694.t90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 73 -
8 g2694.t90 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 74 79 -
15 g2694.t90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 80 102 -
10 g2694.t90 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 103 113 -
16 g2694.t90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 114 135 -
7 g2694.t90 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 136 154 -
5 g2694.t90 SignalP_EUK SignalP-noTM SignalP-noTM 1 17 -
18 g2694.t90 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 18 -
4 g2694.t90 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 17 -
19 g2694.t90 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 116 135 -

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. There were no conditions that were differentially expressed