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.t4 TSS g6000.t4 13447744 13447744
chr_2 g6000 g6000.t4 isoform g6000.t4 13447813 13448805
chr_2 g6000 g6000.t4 exon g6000.t4.exon1 13447813 13448008
chr_2 g6000 g6000.t4 cds g6000.t4.CDS1 13447813 13448008
chr_2 g6000 g6000.t4 exon g6000.t4.exon2 13448139 13448279
chr_2 g6000 g6000.t4 cds g6000.t4.CDS2 13448139 13448279
chr_2 g6000 g6000.t4 exon g6000.t4.exon3 13448342 13448647
chr_2 g6000 g6000.t4 cds g6000.t4.CDS3 13448342 13448647
chr_2 g6000 g6000.t4 exon g6000.t4.exon4 13448711 13448805
chr_2 g6000 g6000.t4 cds g6000.t4.CDS4 13448711 13448805
chr_2 g6000 g6000.t4 TTS g6000.t4 13448951 13448951

Sequences

>g6000.t4 Gene=g6000 Length=738
ATGATTAACATCGCATCAAAGGCTGGAAATTATCTTCGAGCGACGAATCAAGTCGTTTCT
AGTGGCCTAAGACCACTTGCTGGTGCCGCGATCGAAAAGAAAAGTTTAGTAGTTGACAAA
AAAGAATTTTTGACAGTAGAATCACTTGGCAAGGACCTTCCTATTCTTAATCATTATGTT
CAATCTGGATTAACAACAAAGACTCAAGTTCGTTTTGCCCATACTGACATTCAAGTCCCA
GATTTTACTCCATATAGACGTGATTCAACAAAACGAGCAAACGCTAAAGCCCAAACAGCA
GAGGAACGAAAAGCTTTTTCATATGCTCTCGTTGGAGCAACAACTGTAACAACAGCTTAT
GCTGCAAAAGTTTTAGTCACAGACTTTGTCTCATCAATGAGTGCATCAGCTGATGTTCTT
GCTTTGGCCAAGATTGAAATTAAATTGGGAGATATTCCTGAGGGCAAGTCAGTTACATTC
AAATGGAGAGGAAAACCATTGTTTATTCGTCATCGTACAGATGAAGAAATTTCAACTGAA
CAATCGGTCAATCTATCTGAACTCAGAGACGCTCAGCATGATAGTGAACGTGCAACAGAC
CCAAAATGGTTGGTCGTTATTGGAGTGTGCACTCACTTGGGTTATGATGCTTCTGGACGT
ATTCGAAAAGGACCAGCTCCTCTCAATCTCGAGGTTCCTCCTTACAGTTTTAACGAAGGT
CTCTTAGTTGTCGGTTAA

>g6000.t4 Gene=g6000 Length=245
MINIASKAGNYLRATNQVVSSGLRPLAGAAIEKKSLVVDKKEFLTVESLGKDLPILNHYV
QSGLTTKTQVRFAHTDIQVPDFTPYRRDSTKRANAKAQTAEERKAFSYALVGATTVTTAY
AAKVLVTDFVSSMSASADVLALAKIEIKLGDIPEGKSVTFKWRGKPLFIRHRTDEEISTE
QSVNLSELRDAQHDSERATDPKWLVVIGVCTHLGYDASGRIRKGPAPLNLEVPPYSFNEG
LLVVG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g6000.t4 CDD cd03470 Rieske_cytochrome_bc1 144 245 0e+00
9 g6000.t4 Gene3D G3DSA:1.20.5.270 - 73 135 0e+00
7 g6000.t4 Gene3D G3DSA:2.102.10.10 - 137 214 0e+00
8 g6000.t4 Gene3D G3DSA:2.102.10.10 - 215 245 1e-05
3 g6000.t4 PANTHER PTHR10134 CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL 68 214 0e+00
4 g6000.t4 PANTHER PTHR10134 CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL 215 245 0e+00
1 g6000.t4 Pfam PF09165 Ubiquinol-cytochrome c reductase 8 kDa, N-terminal 3 71 0e+00
2 g6000.t4 Pfam PF02921 Ubiquinol cytochrome reductase transmembrane region 74 138 0e+00
5 g6000.t4 SUPERFAMILY SSF81502 ISP transmembrane anchor 73 140 0e+00
6 g6000.t4 SUPERFAMILY SSF50022 ISP domain 127 244 0e+00

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

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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