General information for g4078.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytochrome c oxidase assembly factor 7-like protein.
Parent gene
- The parent gene g4078 is located on chr_3: 30467590..30468941 (+ 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 | g4078 | g4078.t1 | TSS | g4078.t1 | 30466709 | 30466709 |
| chr_3 | g4078 | g4078.t1 | isoform | g4078.t1 | 30466779 | 30467590 |
| chr_3 | g4078 | g4078.t1 | exon | g4078.t1.exon1 | 30466779 | 30466878 |
| chr_3 | g4078 | g4078.t1 | cds | g4078.t1.CDS1 | 30466779 | 30466878 |
| chr_3 | g4078 | g4078.t1 | exon | g4078.t1.exon2 | 30466935 | 30467590 |
| chr_3 | g4078 | g4078.t1 | cds | g4078.t1.CDS2 | 30466935 | 30467590 |
| chr_3 | g4078 | g4078.t1 | TTS | g4078.t1 | 30467678 | 30467678 |
Sequences
>g4078.t1 Gene=g4078 Length=756
ATGGCATTTGATCTGAAAAATGAAGCTGATGTAAAAGAATATATAGAGAAACTAGGAATT
GAGTATCGTTTTGGCTGTTACTCAGAGAAAAAGCCTGAAGTATGTCATCTACTTGGTGAT
TATCTTGAGAGCATTAAAAAGGATTTTGAAAAAGCGGCAAAAGTATATCGAGCAAATTGT
GATGATTATGGTCATGCGAAGTCGTGTCTAAAATTTGGTCATTATAGTTTCTTAGGCAAA
GGTAAATCTTCCAGCATCGAAAAAGGAGACCCGAAACAAGCGTTTCAATATTATAAAAAA
GGCTGTGAGCTCAAAGATGCTGATTGTTGCTTACATAGTGGTCTGCTCATGGTAAGCAGG
ACTAAACCTGCACTTGTCGAACGCGATGTAATTAAAGGAATGGATGCTCTTCAAAAAAGT
TGTTCGCTCAATAATGGAACTGCATGCTTCTATTTATCTGGCATGTTTATATCTGGTGTT
TTTAAAAATGAAGATGCAAAGAAATCTGCAAAACCTGAACCAAGTGAATTTTTAATTCCA
AAAGATATGAAGAAAGCATTTGAATTTGCAACTAAAGCTTGTGAACTTGACAACATGTAT
GCATGCTCTAATCTATCACAGATGTATTCTAAAGGCGATGGCACAGAAAAGAATGATAAG
AAAGCTGAACATTTTAAAAAGAAGGCTTTAGATATGCAAGATCAATTAAAGAAACAACAT
GAAGAAGTTAAATTTCAACAAGGACTGGGTGTGTAA
>g4078.t1 Gene=g4078 Length=251
MAFDLKNEADVKEYIEKLGIEYRFGCYSEKKPEVCHLLGDYLESIKKDFEKAAKVYRANC
DDYGHAKSCLKFGHYSFLGKGKSSSIEKGDPKQAFQYYKKGCELKDADCCLHSGLLMVSR
TKPALVERDVIKGMDALQKSCSLNNGTACFYLSGMFISGVFKNEDAKKSAKPEPSEFLIP
KDMKKAFEFATKACELDNMYACSNLSQMYSKGDGTEKNDKKAEHFKKKALDMQDQLKKQH
EEVKFQQGLGV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4078.t1 | Coils | Coil | Coil | 222 | 242 | - |
| 10 | g4078.t1 | Gene3D | G3DSA:1.25.40.10 | - | 2 | 248 | 4.0E-33 |
| 4 | g4078.t1 | PANTHER | PTHR13891 | UNCHARACTERIZED | 4 | 246 | 5.0E-69 |
| 2 | g4078.t1 | Pfam | PF08238 | Sel1 repeat | 78 | 105 | 0.019 |
| 1 | g4078.t1 | Pfam | PF08238 | Sel1 repeat | 179 | 198 | 0.42 |
| 3 | g4078.t1 | Pfam | PF08238 | Sel1 repeat | 201 | 232 | 0.0072 |
| 8 | g4078.t1 | SMART | SM00671 | sel1 | 32 | 64 | 200.0 |
| 7 | g4078.t1 | SMART | SM00671 | sel1 | 66 | 106 | 14.0 |
| 9 | g4078.t1 | SMART | SM00671 | sel1 | 146 | 198 | 27.0 |
| 6 | g4078.t1 | SMART | SM00671 | sel1 | 199 | 234 | 9.2E-6 |
| 5 | g4078.t1 | SUPERFAMILY | SSF81901 | HCP-like | 87 | 234 | 6.41E-23 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K18180 (cytochrome c oxidase assembly factor 7)
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.
