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.t2 isoform g11746.t2 18215567 18216491
chr_1 g11746 g11746.t2 exon g11746.t2.exon1 18215567 18216491
chr_1 g11746 g11746.t2 TTS g11746.t2 18215570 18215570
chr_1 g11746 g11746.t2 cds g11746.t2.CDS1 18215645 18216487
chr_1 g11746 g11746.t2 TSS g11746.t2 18216906 18216906

Sequences

>g11746.t2 Gene=g11746 Length=925
GGAAATGACACTGGAAGAATTTAAGTTTATTTTCTGGATGGAATATGGTCATCGTATGTG
GGGTCGACTCATTGGTGCAATGTTTGCAATTCCTGCTGCTTATTTTTGGTCGAAAGGTTA
TTTCAATAAGGCAATGAAAATAAAAGTAGGAATTTTTGGAACTCTTATTGGTTTGCAAGG
ACTTATGGGCTGGTATATGGTTAAGTCAGGTCTAGAAGATAGATTTCACGGAGAAAATGA
TGTTCCTCGCGTATCACAATATCGATTAGCTGCTCATTTGTCGTTTGCATTCGCACTTTA
TATCTTATTCCTGATGTCATCGTTAGACCACTTACTGCCAACTAAACAACAAGCTATTGA
AGTAACTGCAAATGCACTTAAATTGAGAAAACTCGCTCACATCTCGAAAGGAATGGTGTT
TCTCACAGCTGTCTCTGGTGCATTTGTTGCAGGTTTAGATGCTGGCTTAGTTTACAATTC
TTTCCCAAAGTTTGCTGATCGATGGATTCCTAGTGATTTACTCGCTTTCTCGCCTACTAT
TAAAAATTTTACTGAAAATCCAACTACTGTTCAATTTGATCATCGCATTTTAGGTACATC
GACTCTTGCTCTAATAACTGGAATGTACATGCTTTCAAGAAAATGTAAACTGCCAAATCG
CGCTCATACAGCAGCAACAGCAGTTGTTTTAATGGGTTGGGCACAAGTAATTTTGGGAAT
TTCAACACTATTAACATATGTGCCTGTTACATTAGCTACAAGCCATCAATCTGGTTCATT
AATTTTACTTAGCATGGCTGTATGGCTTACACATGAGTTGAAGTGGTTAAAAAAGATACC
TAAATAGAAAATAGTTTAAGTCAAAGTAATTTACAATATTGTAGAAAAATGCATTTAATA
AATCTGATGAAATTTCAAATTAAAA

>g11746.t2 Gene=g11746 Length=280
MTLEEFKFIFWMEYGHRMWGRLIGAMFAIPAAYFWSKGYFNKAMKIKVGIFGTLIGLQGL
MGWYMVKSGLEDRFHGENDVPRVSQYRLAAHLSFAFALYILFLMSSLDHLLPTKQQAIEV
TANALKLRKLAHISKGMVFLTAVSGAFVAGLDAGLVYNSFPKFADRWIPSDLLAFSPTIK
NFTENPTTVQFDHRILGTSTLALITGMYMLSRKCKLPNRAHTAATAVVLMGWAQVILGIS
TLLTYVPVTLATSHQSGSLILLSMAVWLTHELKWLKKIPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g11746.t2 PANTHER PTHR23289 CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX15 1 275 6.9E-119
1 g11746.t2 Pfam PF02628 Cytochrome oxidase assembly protein 1 266 2.1E-74
16 g11746.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 17 -
21 g11746.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 18 36 -
12 g11746.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 37 47 -
18 g11746.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 48 66 -
15 g11746.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 67 85 -
17 g11746.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 86 104 -
11 g11746.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 105 135 -
22 g11746.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 136 157 -
13 g11746.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 158 194 -
19 g11746.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 195 211 -
10 g11746.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 212 222 -
23 g11746.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 223 246 -
14 g11746.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 247 257 -
20 g11746.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 258 275 -
9 g11746.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 276 280 -
8 g11746.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 18 35 -
6 g11746.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 48 65 -
3 g11746.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 85 107 -
5 g11746.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 136 158 -
4 g11746.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 194 211 -
7 g11746.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 224 246 -

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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