General information for g10248.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytochrome c oxidase assembly protein COX18, mitochondrial.
Parent gene
- The parent gene g10248 is located on chr_1: 8521057..8522122 (+ 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_1 | g10248 | g10248.t1 | TSS | g10248.t1 | 8521002 | 8521002 |
| chr_1 | g10248 | g10248.t1 | isoform | g10248.t1 | 8521057 | 8522122 |
| chr_1 | g10248 | g10248.t1 | exon | g10248.t1.exon1 | 8521057 | 8521758 |
| chr_1 | g10248 | g10248.t1 | cds | g10248.t1.CDS1 | 8521057 | 8521758 |
| chr_1 | g10248 | g10248.t1 | exon | g10248.t1.exon2 | 8521841 | 8522122 |
| chr_1 | g10248 | g10248.t1 | cds | g10248.t1.CDS2 | 8521841 | 8522122 |
| chr_1 | g10248 | g10248.t1 | TTS | g10248.t1 | 8522157 | 8522157 |
Sequences
>g10248.t1 Gene=g10248 Length=984
ATGAATAAAATATTATTTTCTGAAGTAGTATTGTTAAGAAAATATGCAGTGCACGCTTCA
TTAGCTGCTCGTTATCCAAATTATACCATAAATCAAATAAATCATGATCAGAGAAGAAAT
TTCACTCAAGATTTTTGGCAGTCGGTTTCTTCGAGTAAATTAGTCAATGTTTTACAAGAA
GCTACAATACAACTGCACGATACTTCAGGTTTGCCTTGGTGGTCCACAATTATTATTTCG
ACTGTATTATTAAGAGGGTGCATCACTTTGCCACTCGCATTGTATCAAAATAGAATATTA
GCAAAAGTTGAGCGAGTCACAAAAGAACTACCGGATCTTGTCAATGAGTTAAAAATGGAA
ACTGCTATAGCAACAAAAAAATTTAATTGGACAGAACAACAAGCAAAAGCCATGTATAAT
AATTCACTCAACAAATTATGGAAAGATTTGCTTGTTAGAGATAATTGTCATCCTATGAAA
TCAGCAATTGTCTTAGTTTTTCAAATTCCACTCTGGATTTGTCAATCTGTTGCAATAAGA
AATATGTTATATATGCAACCCGATCCTACATCAATTCAAGCTCAAATTGTATGTGCTGAA
ATGTCTTTGGGTGGTATTGCATGGTTTCCAAATTTAGTCGAAGTTGATCACTCATTTATT
CTGCCAGTGGCTCTCGGTCTTATTAATTTAGCTGTTCTCGAGATTCAGACCATGAGTAGA
AAAATACAAGTAAACAGTAAATTACAAAAATACGGTCAATATTTCTTTAGAGGAATCAGC
ATATTGATGGTACCCGTTGCAGCTTTTGTTCCATCAGGAGTAGCACTTTATTGGGTGTCT
TCAAGCACATTTGGTTTATTACAGAATTTATTTATTTTATCTCCAAAAGTTAGACGTTTG
GCAAGAATACCAAAAGTAGATAGTGAACATGAGCATCCTTATAAACACATAATTTGTAAA
ATTAGAGAACGTATAGGCAAATAA
>g10248.t1 Gene=g10248 Length=327
MNKILFSEVVLLRKYAVHASLAARYPNYTINQINHDQRRNFTQDFWQSVSSSKLVNVLQE
ATIQLHDTSGLPWWSTIIISTVLLRGCITLPLALYQNRILAKVERVTKELPDLVNELKME
TAIATKKFNWTEQQAKAMYNNSLNKLWKDLLVRDNCHPMKSAIVLVFQIPLWICQSVAIR
NMLYMQPDPTSIQAQIVCAEMSLGGIAWFPNLVEVDHSFILPVALGLINLAVLEIQTMSR
KIQVNSKLQKYGQYFFRGISILMVPVAAFVPSGVALYWVSSSTFGLLQNLFILSPKVRRL
ARIPKVDSEHEHPYKHIICKIRERIGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g10248.t1 | PANTHER | PTHR12428 | OXA1 | 39 | 319 | 4.3E-73 |
| 3 | g10248.t1 | PANTHER | PTHR12428:SF51 | CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX18, MITOCHONDRIAL | 39 | 319 | 4.3E-73 |
| 1 | g10248.t1 | Pfam | PF02096 | 60Kd inner membrane protein | 73 | 292 | 2.6E-12 |
| 12 | g10248.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 72 | - |
| 18 | g10248.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 95 | - |
| 8 | g10248.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 96 | 161 | - |
| 16 | g10248.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 162 | 179 | - |
| 11 | g10248.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 180 | 216 | - |
| 14 | g10248.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 217 | 233 | - |
| 9 | g10248.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 234 | 253 | - |
| 15 | g10248.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 254 | 270 | - |
| 13 | g10248.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 271 | 275 | - |
| 17 | g10248.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 276 | 293 | - |
| 10 | g10248.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 294 | 327 | - |
| 7 | g10248.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 95 | - |
| 5 | g10248.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 162 | 179 | - |
| 4 | g10248.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 218 | 235 | - |
| 6 | g10248.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 256 | 278 | - |
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:0032977 | membrane insertase activity | MF |
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K17797 (mitochondrial inner membrane protein COX18)
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.
