General information for g6660.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g6660 is located on chr_2: 17983351..17983695 (- 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 | g6660 | g6660.t1 | TTS | g6660.t1 | 17982168 | 17982168 |
| chr_2 | g6660 | g6660.t1 | isoform | g6660.t1 | 17983351 | 17983695 |
| chr_2 | g6660 | g6660.t1 | exon | g6660.t1.exon1 | 17983351 | 17983472 |
| chr_2 | g6660 | g6660.t1 | cds | g6660.t1.CDS1 | 17983351 | 17983472 |
| chr_2 | g6660 | g6660.t1 | exon | g6660.t1.exon2 | 17983542 | 17983695 |
| chr_2 | g6660 | g6660.t1 | cds | g6660.t1.CDS2 | 17983542 | 17983695 |
| chr_2 | g6660 | g6660.t1 | TSS | g6660.t1 | 17983717 | 17983717 |
Sequences
>g6660.t1 Gene=g6660 Length=276
ATGTCTGATCAAAAAAAAGAAACAACAAATAAAGTCAAGCATTTAGACCGAAAATTAAAG
CAAACAGAAATTGATTTTATGAAATTAATAGAAGAGCAGAACGTGCAGCGTGTTTTAAAA
TTGAAGAAGACTAGAAAGAATAACATTTTAACTGGCATAGCTCTTGGAATATCCGTTTTG
AGTATTTATGGTTATTCTATGTATGCGGTGAAACAAGAAAAGTTTTTAGACGATTTTGAA
GAACCGGCAAAAGAAGAGATTTCACAATCCCAATAA
>g6660.t1 Gene=g6660 Length=91
MSDQKKETTNKVKHLDRKLKQTEIDFMKLIEEQNVQRVLKLKKTRKNNILTGIALGISVL
SIYGYSMYAVKQEKFLDDFEEPAKEEISQSQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g6660.t1 | Coils | Coil | Coil | 5 | 32 | - |
| 2 | g6660.t1 | PANTHER | PTHR15642 | CYTOCHROME C OXIDASE ASSEMBLY FACTOR 3, MITOCHONDRIAL | 5 | 90 | 1.6E-15 |
| 1 | g6660.t1 | Pfam | PF09813 | Coiled-coil domain-containing protein 56 | 7 | 86 | 1.0E-28 |
| 5 | g6660.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 48 | - |
| 7 | g6660.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 49 | 68 | - |
| 6 | g6660.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 69 | 91 | - |
| 3 | g6660.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 47 | 69 | - |
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:0033617 | mitochondrial cytochrome c oxidase assembly | BP |
KEGG
Orthology
- This transcript has been annotated with K18175 (cytochrome c oxidase assembly factor 3, animal type)
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.
