General information for g11746.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytochrome c oxidase assembly protein COX15-like protein.
Parent gene
- The parent gene g11746 is located on chr_1: 18216744..18217303 (- 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 | g11746 | g11746.t1 | TTS | g11746.t1 | 18215570 | 18215570 |
| chr_1 | g11746 | g11746.t1 | isoform | g11746.t1 | 18215645 | 18217204 |
| chr_1 | g11746 | g11746.t1 | exon | g11746.t1.exon1 | 18215645 | 18216500 |
| chr_1 | g11746 | g11746.t1 | cds | g11746.t1.CDS1 | 18215645 | 18216500 |
| chr_1 | g11746 | g11746.t1 | exon | g11746.t1.exon2 | 18216563 | 18216695 |
| chr_1 | g11746 | g11746.t1 | cds | g11746.t1.CDS2 | 18216563 | 18216695 |
| chr_1 | g11746 | g11746.t1 | exon | g11746.t1.exon3 | 18216851 | 18216989 |
| chr_1 | g11746 | g11746.t1 | cds | g11746.t1.CDS3 | 18216851 | 18216989 |
| chr_1 | g11746 | g11746.t1 | exon | g11746.t1.exon4 | 18217049 | 18217204 |
| chr_1 | g11746 | g11746.t1 | cds | g11746.t1.CDS4 | 18217049 | 18217204 |
| chr_1 | g11746 | g11746.t1 | TSS | g11746.t1 | 18217370 | 18217370 |
Sequences
>g11746.t1 Gene=g11746 Length=1284
ATGATTCTTAATTCTTGTCTGATTTCAAGAAATTTGTTTAGAAATACAAGTTTATTGTTT
TGTAAAAAATCATTTACAAACATAAACAACAGAAACATTTATAGATCCTCTCTATTGCAA
AGTCAATCCAGTTTGCTTATACCAAAGAATAATAAGATTAAAAACATACTAACTTTAAGA
CAAACAATAAAAGGATTCTGTACAAAGGCAAATGAATCAACTACTAAAGGACAAAAGGCA
GTAGGATGGTGGCTTGCAGGCTGTTCAGGCATGGTTTTTGTGGCTGTTGCATTAGGTGGT
ATAACAAGATTAACTGAATCGGGTCTTTCAATGTCACATTGGAAGTTATTAGGAGAAAAG
CCACCTACTACTCAAGAAGATTGGATTCGTGAATTTGAAATTTATAAACAGTTTCCAGAA
TTTAAAATCAAAAATAAGGAAATGACACTGGAAGAATTTAAGTTTATTTTCTGGATGGAA
TATGGTCATCGTATGTGGGGTCGACTCATTGGTGCAATGTTTGCAATTCCTGCTGCTTAT
TTTTGGTCGAAAGGTTATTTCAATAAGGCAATGAAAATAAAAGTAGGAATTTTTGGAACT
CTTATTGGTTTGCAAGGACTTATGGGCTGGTATATGGTTAAGTCAGGTCTAGAAGATAGA
TTTCACGGAGAAAATGATGTTCCTCGCGTATCACAATATCGATTAGCTGCTCATTTGTCG
TTTGCATTCGCACTTTATATCTTATTCCTGATGTCATCGTTAGACCACTTACTGCCAACT
AAACAACAAGCTATTGAAGTAACTGCAAATGCACTTAAATTGAGAAAACTCGCTCACATC
TCGAAAGGAATGGTGTTTCTCACAGCTGTCTCTGGTGCATTTGTTGCAGGTTTAGATGCT
GGCTTAGTTTACAATTCTTTCCCAAAGTTTGCTGATCGATGGATTCCTAGTGATTTACTC
GCTTTCTCGCCTACTATTAAAAATTTTACTGAAAATCCAACTACTGTTCAATTTGATCAT
CGCATTTTAGGTACATCGACTCTTGCTCTAATAACTGGAATGTACATGCTTTCAAGAAAA
TGTAAACTGCCAAATCGCGCTCATACAGCAGCAACAGCAGTTGTTTTAATGGGTTGGGCA
CAAGTAATTTTGGGAATTTCAACACTATTAACATATGTGCCTGTTACATTAGCTACAAGC
CATCAATCTGGTTCATTAATTTTACTTAGCATGGCTGTATGGCTTACACATGAGTTGAAG
TGGTTAAAAAAGATACCTAAATAG
>g11746.t1 Gene=g11746 Length=427
MILNSCLISRNLFRNTSLLFCKKSFTNINNRNIYRSSLLQSQSSLLIPKNNKIKNILTLR
QTIKGFCTKANESTTKGQKAVGWWLAGCSGMVFVAVALGGITRLTESGLSMSHWKLLGEK
PPTTQEDWIREFEIYKQFPEFKIKNKEMTLEEFKFIFWMEYGHRMWGRLIGAMFAIPAAY
FWSKGYFNKAMKIKVGIFGTLIGLQGLMGWYMVKSGLEDRFHGENDVPRVSQYRLAAHLS
FAFALYILFLMSSLDHLLPTKQQAIEVTANALKLRKLAHISKGMVFLTAVSGAFVAGLDA
GLVYNSFPKFADRWIPSDLLAFSPTIKNFTENPTTVQFDHRILGTSTLALITGMYMLSRK
CKLPNRAHTAATAVVLMGWAQVILGISTLLTYVPVTLATSHQSGSLILLSMAVWLTHELK
WLKKIPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g11746.t1 | PANTHER | PTHR23289 | CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX15 | 45 | 422 | 9.9E-161 |
| 1 | g11746.t1 | Pfam | PF02628 | Cytochrome oxidase assembly protein | 83 | 413 | 2.8E-99 |
| 10 | g11746.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 80 | - |
| 25 | g11746.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 101 | - |
| 17 | g11746.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 102 | 164 | - |
| 19 | g11746.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 165 | 183 | - |
| 14 | g11746.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 184 | 194 | - |
| 22 | g11746.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 195 | 213 | - |
| 16 | g11746.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 214 | 232 | - |
| 26 | g11746.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 233 | 251 | - |
| 11 | g11746.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 252 | 282 | - |
| 23 | g11746.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 304 | - |
| 15 | g11746.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 305 | 341 | - |
| 21 | g11746.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 342 | 358 | - |
| 13 | g11746.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 359 | 369 | - |
| 20 | g11746.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 370 | 393 | - |
| 18 | g11746.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 394 | 404 | - |
| 24 | g11746.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 405 | 422 | - |
| 12 | g11746.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 423 | 427 | - |
| 4 | g11746.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 102 | - |
| 5 | g11746.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 165 | 182 | - |
| 9 | g11746.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 195 | 212 | - |
| 8 | g11746.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 254 | - |
| 3 | g11746.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 305 | - |
| 6 | g11746.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 341 | 358 | - |
| 7 | g11746.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 371 | 393 | - |
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:0016627 | oxidoreductase activity, acting on the CH-CH group of donors | MF |
| GO:0016020 | membrane | CC |
| GO:0006784 | heme A biosynthetic process | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K02259 (heme a synthase)
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.
