General information for g3436.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3436 is located on chr_3: 25447064..25447930 (- 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 | g3436 | g3436.t1 | TTS | g3436.t1 | 25446980 | 25446980 |
| chr_3 | g3436 | g3436.t1 | isoform | g3436.t1 | 25447064 | 25447930 |
| chr_3 | g3436 | g3436.t1 | exon | g3436.t1.exon1 | 25447064 | 25447200 |
| chr_3 | g3436 | g3436.t1 | cds | g3436.t1.CDS1 | 25447064 | 25447200 |
| chr_3 | g3436 | g3436.t1 | exon | g3436.t1.exon2 | 25447261 | 25447308 |
| chr_3 | g3436 | g3436.t1 | cds | g3436.t1.CDS2 | 25447261 | 25447308 |
| chr_3 | g3436 | g3436.t1 | exon | g3436.t1.exon3 | 25447379 | 25447411 |
| chr_3 | g3436 | g3436.t1 | cds | g3436.t1.CDS3 | 25447379 | 25447411 |
| chr_3 | g3436 | g3436.t1 | exon | g3436.t1.exon4 | 25447480 | 25447518 |
| chr_3 | g3436 | g3436.t1 | cds | g3436.t1.CDS4 | 25447480 | 25447518 |
| chr_3 | g3436 | g3436.t1 | exon | g3436.t1.exon5 | 25447726 | 25447785 |
| chr_3 | g3436 | g3436.t1 | cds | g3436.t1.CDS5 | 25447726 | 25447785 |
| chr_3 | g3436 | g3436.t1 | exon | g3436.t1.exon6 | 25447840 | 25447930 |
| chr_3 | g3436 | g3436.t1 | cds | g3436.t1.CDS6 | 25447840 | 25447930 |
| chr_3 | g3436 | g3436.t1 | TSS | g3436.t1 | 25448014 | 25448014 |
Sequences
>g3436.t1 Gene=g3436 Length=408
ATGATATCAAATAGAGCTTTATGGAAAACTTCAGTCTATATTGCGATCGGTGGTATGACC
AGTGTCATGATTATGAGATCAATTTTAAAAGATAGAGTACGAAAAACAGAATATTATAGA
GAAGCATTTAAAAAATTAAGAGCTCATGAAGGTGCACAATTTCTACTTGGCGAACCGATT
AAAGAAGCTGGCTTTGATATAGGAAAACCAAATTATGCTGACGCAAAAGAGGCATACTTT
GAAATTGGTGTAAAAGGACCAAAAAATATTGGAAAAATGTACTTTTGGGCAGTGTCTGAA
AATGAGAAGTGGACTATTGATCGATTGGAGCTAGAGCTTAGAAATGATGATAAACGTTTG
GCTATTGTAAAAAAGGCACATGATGCTGAAGTTGTAAAAAATGAATAA
>g3436.t1 Gene=g3436 Length=135
MISNRALWKTSVYIAIGGMTSVMIMRSILKDRVRKTEYYREAFKKLRAHEGAQFLLGEPI
KEAGFDIGKPNYADAKEAYFEIGVKGPKNIGKMYFWAVSENEKWTIDRLELELRNDDKRL
AIVKKAHDAEVVKNE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g3436.t1 | Coils | Coil | Coil | 106 | 126 | - |
| 2 | g3436.t1 | PANTHER | PTHR47148 | CYTOCHROME C OXIDASE ASSEMBLY FACTOR 1 HOMOLOG | 1 | 129 | 3.6E-26 |
| 1 | g3436.t1 | Pfam | PF08695 | Cytochrome oxidase complex assembly protein 1 | 12 | 123 | 1.4E-16 |
| 6 | g3436.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 7 | g3436.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 29 | - |
| 5 | g3436.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 30 | 135 | - |
| 3 | g3436.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 29 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K18173 (cytochrome c oxidase assembly factor 1)
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.
