Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytochrome b-c1 complex subunit Rieske, 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 g6000 g6000.t7 TSS g6000.t7 13447744 13447744
chr_2 g6000 g6000.t7 isoform g6000.t7 13447813 13448805
chr_2 g6000 g6000.t7 exon g6000.t7.exon1 13447813 13448279
chr_2 g6000 g6000.t7 exon g6000.t7.exon2 13448342 13448805
chr_2 g6000 g6000.t7 cds g6000.t7.CDS1 13448401 13448805
chr_2 g6000 g6000.t7 TTS g6000.t7 13448951 13448951

Sequences

>g6000.t7 Gene=g6000 Length=931
ATGATTAACATCGCATCAAAGGCTGGAAATTATCTTCGAGCGACGAATCAAGTCGTTTCT
AGTGGCCTAAGACCACTTGCTGGTGCCGCGATCGAAAAGAAAAGTTTAGTAGTTGACAAA
AAAGAATTTTTGACAGTAGAATCACTTGGCAAGGACCTTCCTATTCTTAATCATTATGTT
CAATCTGGATTAACAAGTAAGTATATGACATTAAATTATGCTATCCAACATTTTGCTTCA
GTCTTTAATGAATTTTCAAAAAATTATATAACCAACTCACAACAACGTCAATTCATAAAT
TATTATCCTTGTCTTATTTATTACAGCAAAGACTCAAGTTCGTTTTGCCCATACTGACAT
TCAAGTCCCAGATTTTACTCCATATAGACGTGATTCAACAAAACGAGCAAACGCTAAAGC
CCAAACAGCAGAGGAACGAAAAGCTTTTTCATATGCTCTCGTTGGAGCAACAACTGTAAC
AACAGCTTATGCTGCAAAAGTTTTAGTCACAGACTTTGTCTCATCAATGAGTGCATCAGC
TGATGTTCTTGCTTTGGCCAAGATTGAAATTAAATTGGGAGATATTCCTGAGGGCAAGTC
AGTTACATTCAAATGGAGAGGAAAACCATTGTTTATTCGTCATCGTACAGATGAAGAAAT
TTCAACTGAACAATCGGTCAATCTATCTGAACTCAGAGACGCTCAGCATGATAGTGAACG
TGCAACAGACCCAAAATGGTTGGTCGTTATTGGAGTGTGCACTCACTTGGGTTGTGTGCC
TATTGCAAATGCTGGAGAATTTGGAGGCTACTATTGCCCATGCCATGGTTCACATTATGA
TGCTTCTGGACGTATTCGAAAAGGACCAGCTCCTCTCAATCTCGAGGTTCCTCCTTACAG
TTTTAACGAAGGTCTCTTAGTTGTCGGTTAA

>g6000.t7 Gene=g6000 Length=134
MSASADVLALAKIEIKLGDIPEGKSVTFKWRGKPLFIRHRTDEEISTEQSVNLSELRDAQ
HDSERATDPKWLVVIGVCTHLGCVPIANAGEFGGYYCPCHGSHYDASGRIRKGPAPLNLE
VPPYSFNEGLLVVG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6000.t7 CDD cd03470 Rieske_cytochrome_bc1 12 134 0.000
7 g6000.t7 Gene3D G3DSA:2.102.10.10 - 5 134 0.000
2 g6000.t7 PANTHER PTHR10134 CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL 1 134 0.000
4 g6000.t7 PRINTS PR00162 Rieske 2Fe-2S subunit signature 73 84 0.000
5 g6000.t7 PRINTS PR00162 Rieske 2Fe-2S subunit signature 95 107 0.000
3 g6000.t7 PRINTS PR00162 Rieske 2Fe-2S subunit signature 107 119 0.000
1 g6000.t7 Pfam PF00355 Rieske [2Fe-2S] domain 18 122 0.000
9 g6000.t7 ProSiteProfiles PS51296 Rieske [2Fe-2S] iron-sulfur domain profile. 65 133 21.187
6 g6000.t7 SUPERFAMILY SSF50022 ISP domain 3 133 0.000
10 g6000.t7 TIGRFAM TIGR01416 Rieske_proteo: ubiquinol-cytochrome c reductase, iron-sulfur subunit 1 128 0.000

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:0051537 2 iron, 2 sulfur cluster binding MF
GO:0008121 ubiquinol-cytochrome-c reductase activity MF
GO:0055114 NA NA

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