General information for g3984.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g3984 is located on chr_3: 29381375..29381975 (+ 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_3 | g3984 | g3984.t1 | TSS | g3984.t1 | 29381309 | 29381309 |
| chr_3 | g3984 | g3984.t1 | isoform | g3984.t1 | 29381375 | 29381975 |
| chr_3 | g3984 | g3984.t1 | exon | g3984.t1.exon1 | 29381375 | 29381591 |
| chr_3 | g3984 | g3984.t1 | cds | g3984.t1.CDS1 | 29381375 | 29381591 |
| chr_3 | g3984 | g3984.t1 | exon | g3984.t1.exon2 | 29381959 | 29381975 |
| chr_3 | g3984 | g3984.t1 | cds | g3984.t1.CDS2 | 29381959 | 29381975 |
| chr_3 | g3984 | g3984.t1 | TTS | g3984.t1 | NA | NA |
Sequences
>g3984.t1 Gene=g3984 Length=234
ATGGCACCAAAGGAAATTGAGCTCAAGACAGCACCTTTTGACCCACGTTTCCCAAACACA
AATCAGACGCTCTATTGTTATCAGAGCTATATTGATTTCCATCGCTGTGAAAAAGTTAAG
GGGCCAGGAGCAGAGGTGTGCGCTTATTTCAAACGCTGCTATCAATCAATGTGTCCAAAT
GCATGGGTTGAAAAATGGGATACACAACGCGAACAAGATATCAAACTCGATTAA
>g3984.t1 Gene=g3984 Length=77
MAPKEIELKTAPFDPRFPNTNQTLYCYQSYIDFHRCEKVKGPGAEVCAYFKRCYQSMCPN
AWVEKWDTQREQDIKLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3984.t1 | CDD | cd00926 | Cyt_c_Oxidase_VIb | 4 | 73 | 0 |
| 5 | g3984.t1 | Gene3D | G3DSA:1.10.10.140 | Cytochrome C oxidase subunit h | 2 | 75 | 0 |
| 2 | g3984.t1 | PANTHER | PTHR11387:SF2 | CYTOCHROME C OXIDASE SUBUNIT | 4 | 73 | 0 |
| 3 | g3984.t1 | PANTHER | PTHR11387 | CYTOCHROME C OXIDASE SUBUNIT 6B | 4 | 73 | 0 |
| 1 | g3984.t1 | Pfam | PF02297 | Cytochrome oxidase c subunit VIb | 15 | 72 | 0 |
| 4 | g3984.t1 | SUPERFAMILY | SSF47694 | Cytochrome c oxidase subunit h | 5 | 73 | 0 |
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:0045277 | respiratory chain complex IV | CC |
| GO:0005739 | mitochondrion | CC |
KEGG
Orthology
- This transcript has been annotated with K02267 (cytochrome c oxidase subunit 6b)
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.
