Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytochrome c oxidase assembly protein COX15-like protein.

Parent gene

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.t5 TTS g11746.t5 18215570 18215570
chr_1 g11746 g11746.t5 isoform g11746.t5 18215645 18217204
chr_1 g11746 g11746.t5 exon g11746.t5.exon1 18215645 18216500
chr_1 g11746 g11746.t5 cds g11746.t5.CDS1 18215645 18216500
chr_1 g11746 g11746.t5 exon g11746.t5.exon2 18216563 18216695
chr_1 g11746 g11746.t5 cds g11746.t5.CDS2 18216563 18216695
chr_1 g11746 g11746.t5 exon g11746.t5.exon3 18216851 18217204
chr_1 g11746 g11746.t5 cds g11746.t5.CDS3 18216851 18216875
chr_1 g11746 g11746.t5 TSS g11746.t5 18217370 18217370

Sequences

>g11746.t5 Gene=g11746 Length=1343
ATGATTCTTAATTCTTGTCTGATTTCAAGAAATTTGTTTAGAAATACAAGTTTATTGTTT
TGTAAAAAATCATTTACAAACATAAACAACAGAAACATTTATAGATCCTCTCTATTGCAA
AGTCAATCCAGTTTGCTTATACCAAAGAATAATAAGGTGAATATGATAATATATCAAATG
ATAAAAATCATTAAGATATTTAAATTTAAATTTAGATTAAAAACATACTAACTTTAAGAC
AAACAATAAAAGGATTCTGTACAAAGGCAAATGAATCAACTACTAAAGGACAAAAGGCAG
TAGGATGGTGGCTTGCAGGCTGTTCAGGCATGGTTTTTGTGGCTGTTGCATTAGGTGGTA
TAACAAGATTAACTGAATCGGGTCTTTCAATGTCACATTGGAAGTTATTAGGAGAAAAGC
CACCTACTACTCAAGAAGATTGGATTCGTGAATTTGAAATTTATAAACAGTTTCCAGAAT
TTAAAATCAAAAATAAGGAAATGACACTGGAAGAATTTAAGTTTATTTTCTGGATGGAAT
ATGGTCATCGTATGTGGGGTCGACTCATTGGTGCAATGTTTGCAATTCCTGCTGCTTATT
TTTGGTCGAAAGGTTATTTCAATAAGGCAATGAAAATAAAAGTAGGAATTTTTGGAACTC
TTATTGGTTTGCAAGGACTTATGGGCTGGTATATGGTTAAGTCAGGTCTAGAAGATAGAT
TTCACGGAGAAAATGATGTTCCTCGCGTATCACAATATCGATTAGCTGCTCATTTGTCGT
TTGCATTCGCACTTTATATCTTATTCCTGATGTCATCGTTAGACCACTTACTGCCAACTA
AACAACAAGCTATTGAAGTAACTGCAAATGCACTTAAATTGAGAAAACTCGCTCACATCT
CGAAAGGAATGGTGTTTCTCACAGCTGTCTCTGGTGCATTTGTTGCAGGTTTAGATGCTG
GCTTAGTTTACAATTCTTTCCCAAAGTTTGCTGATCGATGGATTCCTAGTGATTTACTCG
CTTTCTCGCCTACTATTAAAAATTTTACTGAAAATCCAACTACTGTTCAATTTGATCATC
GCATTTTAGGTACATCGACTCTTGCTCTAATAACTGGAATGTACATGCTTTCAAGAAAAT
GTAAACTGCCAAATCGCGCTCATACAGCAGCAACAGCAGTTGTTTTAATGGGTTGGGCAC
AAGTAATTTTGGGAATTTCAACACTATTAACATATGTGCCTGTTACATTAGCTACAAGCC
ATCAATCTGGTTCATTAATTTTACTTAGCATGGCTGTATGGCTTACACATGAGTTGAAGT
GGTTAAAAAAGATACCTAAATAG

>g11746.t5 Gene=g11746 Length=337
MVFVAVALGGITRLTESGLSMSHWKLLGEKPPTTQEDWIREFEIYKQFPEFKIKNKEMTL
EEFKFIFWMEYGHRMWGRLIGAMFAIPAAYFWSKGYFNKAMKIKVGIFGTLIGLQGLMGW
YMVKSGLEDRFHGENDVPRVSQYRLAAHLSFAFALYILFLMSSLDHLLPTKQQAIEVTAN
ALKLRKLAHISKGMVFLTAVSGAFVAGLDAGLVYNSFPKFADRWIPSDLLAFSPTIKNFT
ENPTTVQFDHRILGTSTLALITGMYMLSRKCKLPNRAHTAATAVVLMGWAQVILGISTLL
TYVPVTLATSHQSGSLILLSMAVWLTHELKWLKKIPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g11746.t5 PANTHER PTHR23289 CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX15 1 332 2.0E-151
1 g11746.t5 Pfam PF02628 Cytochrome oxidase assembly protein 1 323 2.3E-97
17 g11746.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
18 g11746.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
19 g11746.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 12 -
27 g11746.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 17 -
13 g11746.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 74 -
26 g11746.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 75 93 -
10 g11746.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 94 104 -
21 g11746.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 105 123 -
16 g11746.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 124 142 -
20 g11746.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 143 161 -
11 g11746.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 162 192 -
25 g11746.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 193 214 -
14 g11746.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 215 251 -
23 g11746.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 252 268 -
9 g11746.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 269 279 -
24 g11746.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 280 303 -
15 g11746.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 304 314 -
22 g11746.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 315 332 -
12 g11746.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 333 337 -
7 g11746.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 75 92 -
8 g11746.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 122 -
6 g11746.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 142 164 -
3 g11746.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 193 215 -
5 g11746.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 251 268 -
4 g11746.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 281 303 -

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

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.

Raw TPM values