General information for g6000.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytochrome b-c1 complex subunit Rieske, mitochondrial.
Parent gene
- The parent gene g6000 is located on chr_2: 13448338..13448937 (+ strand)
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.t3 | TSS | g6000.t3 | 13447744 | 13447744 |
| chr_2 | g6000 | g6000.t3 | isoform | g6000.t3 | 13447813 | 13448805 |
| chr_2 | g6000 | g6000.t3 | exon | g6000.t3.exon1 | 13447813 | 13448008 |
| chr_2 | g6000 | g6000.t3 | cds | g6000.t3.CDS1 | 13447813 | 13448008 |
| chr_2 | g6000 | g6000.t3 | exon | g6000.t3.exon2 | 13448151 | 13448279 |
| chr_2 | g6000 | g6000.t3 | cds | g6000.t3.CDS2 | 13448151 | 13448279 |
| chr_2 | g6000 | g6000.t3 | exon | g6000.t3.exon3 | 13448342 | 13448805 |
| chr_2 | g6000 | g6000.t3 | cds | g6000.t3.CDS3 | 13448342 | 13448805 |
| chr_2 | g6000 | g6000.t3 | TTS | g6000.t3 | 13448951 | 13448951 |
Sequences
>g6000.t3 Gene=g6000 Length=789
ATGATTAACATCGCATCAAAGGCTGGAAATTATCTTCGAGCGACGAATCAAGTCGTTTCT
AGTGGCCTAAGACCACTTGCTGGTGCCGCGATCGAAAAGAAAAGTTTAGTAGTTGACAAA
AAAGAATTTTTGACAGTAGAATCACTTGGCAAGGACCTTCCTATTCTTAATCATTATGTT
CAATCTGGATTAACAATTCGTTTTGCCCATACTGACATTCAAGTCCCAGATTTTACTCCA
TATAGACGTGATTCAACAAAACGAGCAAACGCTAAAGCCCAAACAGCAGAGGAACGAAAA
GCTTTTTCATATGCTCTCGTTGGAGCAACAACTGTAACAACAGCTTATGCTGCAAAAGTT
TTAGTCACAGACTTTGTCTCATCAATGAGTGCATCAGCTGATGTTCTTGCTTTGGCCAAG
ATTGAAATTAAATTGGGAGATATTCCTGAGGGCAAGTCAGTTACATTCAAATGGAGAGGA
AAACCATTGTTTATTCGTCATCGTACAGATGAAGAAATTTCAACTGAACAATCGGTCAAT
CTATCTGAACTCAGAGACGCTCAGCATGATAGTGAACGTGCAACAGACCCAAAATGGTTG
GTCGTTATTGGAGTGTGCACTCACTTGGGTTGTGTGCCTATTGCAAATGCTGGAGAATTT
GGAGGCTACTATTGCCCATGCCATGGTTCACATTATGATGCTTCTGGACGTATTCGAAAA
GGACCAGCTCCTCTCAATCTCGAGGTTCCTCCTTACAGTTTTAACGAAGGTCTCTTAGTT
GTCGGTTAA
>g6000.t3 Gene=g6000 Length=262
MINIASKAGNYLRATNQVVSSGLRPLAGAAIEKKSLVVDKKEFLTVESLGKDLPILNHYV
QSGLTIRFAHTDIQVPDFTPYRRDSTKRANAKAQTAEERKAFSYALVGATTVTTAYAAKV
LVTDFVSSMSASADVLALAKIEIKLGDIPEGKSVTFKWRGKPLFIRHRTDEEISTEQSVN
LSELRDAQHDSERATDPKWLVVIGVCTHLGCVPIANAGEFGGYYCPCHGSHYDASGRIRK
GPAPLNLEVPPYSFNEGLLVVG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g6000.t3 | CDD | cd03470 | Rieske_cytochrome_bc1 | 140 | 262 | 0.000 |
| 11 | g6000.t3 | Gene3D | G3DSA:1.20.5.270 | - | 69 | 131 | 0.000 |
| 10 | g6000.t3 | Gene3D | G3DSA:2.102.10.10 | - | 133 | 262 | 0.000 |
| 4 | g6000.t3 | PANTHER | PTHR10134 | CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL | 67 | 262 | 0.000 |
| 6 | g6000.t3 | PRINTS | PR00162 | Rieske 2Fe-2S subunit signature | 201 | 212 | 0.000 |
| 5 | g6000.t3 | PRINTS | PR00162 | Rieske 2Fe-2S subunit signature | 223 | 235 | 0.000 |
| 7 | g6000.t3 | PRINTS | PR00162 | Rieske 2Fe-2S subunit signature | 235 | 247 | 0.000 |
| 2 | g6000.t3 | Pfam | PF09165 | Ubiquinol-cytochrome c reductase 8 kDa, N-terminal | 3 | 65 | 0.000 |
| 3 | g6000.t3 | Pfam | PF02921 | Ubiquinol cytochrome reductase transmembrane region | 70 | 134 | 0.000 |
| 1 | g6000.t3 | Pfam | PF00355 | Rieske [2Fe-2S] domain | 146 | 250 | 0.000 |
| 13 | g6000.t3 | ProSiteProfiles | PS51296 | Rieske [2Fe-2S] iron-sulfur domain profile. | 193 | 261 | 21.187 |
| 8 | g6000.t3 | SUPERFAMILY | SSF81502 | ISP transmembrane anchor | 69 | 136 | 0.000 |
| 9 | g6000.t3 | SUPERFAMILY | SSF50022 | ISP domain | 123 | 261 | 0.000 |
| 14 | g6000.t3 | TIGRFAM | TIGR01416 | Rieske_proteo: ubiquinol-cytochrome c reductase, iron-sulfur subunit | 106 | 256 | 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
- This transcript has been annotated with K00411 (ubiquinol-cytochrome c reductase iron-sulfur subunit)
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