General information for g4812.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytochrome c oxidase assembly protein COX11, mitochondrial.
Parent gene
- The parent gene g4812 is located on chr_2: 5069222..5069977 (+ 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 | g4812 | g4812.t1 | TSS | g4812.t1 | 5069125 | 5069125 |
| chr_2 | g4812 | g4812.t1 | isoform | g4812.t1 | 5069222 | 5069977 |
| chr_2 | g4812 | g4812.t1 | exon | g4812.t1.exon1 | 5069222 | 5069773 |
| chr_2 | g4812 | g4812.t1 | cds | g4812.t1.CDS1 | 5069222 | 5069773 |
| chr_2 | g4812 | g4812.t1 | exon | g4812.t1.exon2 | 5069828 | 5069977 |
| chr_2 | g4812 | g4812.t1 | cds | g4812.t1.CDS2 | 5069828 | 5069977 |
| chr_2 | g4812 | g4812.t1 | TTS | g4812.t1 | 5070031 | 5070031 |
Sequences
>g4812.t1 Gene=g4812 Length=702
ATGTTGAGTTCTCTATTAAGAGCACAGACCAAGTTGATGAGGCATTTAGAAGAAGGGAAC
AAACAGTACTTTTTGCTGTCTCAAATTAAAAATTTTTGTGCACAAGCTCCAAAAAATTCA
CAACAAAATAAGAAATTGAAATCTACACTTTATTATGTCGCTGGAATTGGTGTTCTCACT
GTAGGATTAAGTTATGCAGCTGTTCCATTATATAGAATGTTCTGTTCGGCATATAGTTAT
GGTGGAACAACTGGTGTTCAACATGATGGCTCAAAAGTAGAAGAAATGAAGAAAATTACT
GATAGAATCATTAAAATTAAATTTAATGCCGATCTCGGTGCATCAATGAGATGGAATTTT
AAGCCTCAACAATATGAGATTAAAGTTAGTCCAGGAGAGACTGCTCTTGCATTTTATAAA
GCAACTAATCCAACTGATTTGCCGGTGATAGGAATAAGCACTTATAATGTAATACCTTTC
GAAGCAGGTGCTTATTTTAATAAAATTCAATGCTTTTGCTTTGAAGAGCAGCAACTTAAT
CCACATGAAGAAGTCGACATGCCTGTGTTCTTTTATATCGATCCTGATTTTGTTAATGAT
CCAAAAATGGAATTTGTAGATGAAATTACACTCTCTTACACGTTTTTTGAGAGCAAAGAA
GGTCTAAAACTACCTCTACCTGGCTATGCAAAGCCTCATTAA
>g4812.t1 Gene=g4812 Length=233
MLSSLLRAQTKLMRHLEEGNKQYFLLSQIKNFCAQAPKNSQQNKKLKSTLYYVAGIGVLT
VGLSYAAVPLYRMFCSAYSYGGTTGVQHDGSKVEEMKKITDRIIKIKFNADLGASMRWNF
KPQQYEIKVSPGETALAFYKATNPTDLPVIGISTYNVIPFEAGAYFNKIQCFCFEEQQLN
PHEEVDMPVFFYIDPDFVNDPKMEFVDEITLSYTFFESKEGLKLPLPGYAKPH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4812.t1 | Gene3D | G3DSA:2.60.370.10 | Ctag/Cox11 | 93 | 225 | 9.2E-62 |
| 3 | g4812.t1 | Hamap | MF_00155 | Cytochrome c oxidase assembly protein CtaG [ctaG]. | 26 | 227 | 35.34108 |
| 2 | g4812.t1 | PANTHER | PTHR21320 | CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX11-RELATED | 35 | 219 | 9.8E-73 |
| 1 | g4812.t1 | Pfam | PF04442 | Cytochrome c oxidase assembly protein CtaG/Cox11 | 67 | 217 | 1.4E-58 |
| 7 | g4812.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 49 | - |
| 9 | g4812.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 71 | - |
| 8 | g4812.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 72 | 233 | - |
| 5 | g4812.t1 | SUPERFAMILY | SSF110111 | Ctag/Cox11 | 94 | 220 | 1.31E-54 |
| 4 | g4812.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 49 | 71 | - |
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:0005507 | copper ion binding | MF |
KEGG
Orthology
- This transcript has been annotated with K02258 (cytochrome c oxidase assembly protein subunit 11)
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.
