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.t6 TTS g11746.t6 18215570 18215570
chr_1 g11746 g11746.t6 isoform g11746.t6 18215645 18217204
chr_1 g11746 g11746.t6 exon g11746.t6.exon1 18215645 18216500
chr_1 g11746 g11746.t6 cds g11746.t6.CDS1 18215645 18216500
chr_1 g11746 g11746.t6 exon g11746.t6.exon2 18216563 18216695
chr_1 g11746 g11746.t6 cds g11746.t6.CDS2 18216563 18216660
chr_1 g11746 g11746.t6 exon g11746.t6.exon3 18216752 18216989
chr_1 g11746 g11746.t6 exon g11746.t6.exon4 18217049 18217204
chr_1 g11746 g11746.t6 TSS g11746.t6 18217370 18217370

Sequences

>g11746.t6 Gene=g11746 Length=1383
ATGATTCTTAATTCTTGTCTGATTTCAAGAAATTTGTTTAGAAATACAAGTTTATTGTTT
TGTAAAAAATCATTTACAAACATAAACAACAGAAACATTTATAGATCCTCTCTATTGCAA
AGTCAATCCAGTTTGCTTATACCAAAGAATAATAAGATTAAAAACATACTAACTTTAAGA
CAAACAATAAAAGGATTCTGTACAAAGGCAAATGAATCAACTACTAAAGGACAAAAGGCA
GTAGGATGGTGGCTTGCAGGCTGTTCAGGCATGGTTTTTGTGGCTGTTGCATTAGGTGGG
ACTATACTTTATGGTTTGCTGCTAATATGCGTAATGGTTGTTGTCGATAAAATAATTTAC
AGAACCATTCGCTAAATATGTATCTTAATAAAAAGTGGTATAACAAGATTAACTGAATCG
GGTCTTTCAATGTCACATTGGAAGTTATTAGGAGAAAAGCCACCTACTACTCAAGAAGAT
TGGATTCGTGAATTTGAAATTTATAAACAGTTTCCAGAATTTAAAATCAAAAATAAGGAA
ATGACACTGGAAGAATTTAAGTTTATTTTCTGGATGGAATATGGTCATCGTATGTGGGGT
CGACTCATTGGTGCAATGTTTGCAATTCCTGCTGCTTATTTTTGGTCGAAAGGTTATTTC
AATAAGGCAATGAAAATAAAAGTAGGAATTTTTGGAACTCTTATTGGTTTGCAAGGACTT
ATGGGCTGGTATATGGTTAAGTCAGGTCTAGAAGATAGATTTCACGGAGAAAATGATGTT
CCTCGCGTATCACAATATCGATTAGCTGCTCATTTGTCGTTTGCATTCGCACTTTATATC
TTATTCCTGATGTCATCGTTAGACCACTTACTGCCAACTAAACAACAAGCTATTGAAGTA
ACTGCAAATGCACTTAAATTGAGAAAACTCGCTCACATCTCGAAAGGAATGGTGTTTCTC
ACAGCTGTCTCTGGTGCATTTGTTGCAGGTTTAGATGCTGGCTTAGTTTACAATTCTTTC
CCAAAGTTTGCTGATCGATGGATTCCTAGTGATTTACTCGCTTTCTCGCCTACTATTAAA
AATTTTACTGAAAATCCAACTACTGTTCAATTTGATCATCGCATTTTAGGTACATCGACT
CTTGCTCTAATAACTGGAATGTACATGCTTTCAAGAAAATGTAAACTGCCAAATCGCGCT
CATACAGCAGCAACAGCAGTTGTTTTAATGGGTTGGGCACAAGTAATTTTGGGAATTTCA
ACACTATTAACATATGTGCCTGTTACATTAGCTACAAGCCATCAATCTGGTTCATTAATT
TTACTTAGCATGGCTGTATGGCTTACACATGAGTTGAAGTGGTTAAAAAAGATACCTAAA
TAG

>g11746.t6 Gene=g11746 Length=317
MSHWKLLGEKPPTTQEDWIREFEIYKQFPEFKIKNKEMTLEEFKFIFWMEYGHRMWGRLI
GAMFAIPAAYFWSKGYFNKAMKIKVGIFGTLIGLQGLMGWYMVKSGLEDRFHGENDVPRV
SQYRLAAHLSFAFALYILFLMSSLDHLLPTKQQAIEVTANALKLRKLAHISKGMVFLTAV
SGAFVAGLDAGLVYNSFPKFADRWIPSDLLAFSPTIKNFTENPTTVQFDHRILGTSTLAL
ITGMYMLSRKCKLPNRAHTAATAVVLMGWAQVILGISTLLTYVPVTLATSHQSGSLILLS
MAVWLTHELKWLKKIPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g11746.t6 PANTHER PTHR23289 CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX15 1 312 5.2E-138
1 g11746.t6 Pfam PF02628 Cytochrome oxidase assembly protein 3 303 4.6E-86
13 g11746.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 54 -
18 g11746.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 73 -
12 g11746.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 74 84 -
23 g11746.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 103 -
15 g11746.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 104 122 -
21 g11746.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 123 141 -
10 g11746.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 142 172 -
20 g11746.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 173 194 -
14 g11746.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 195 231 -
17 g11746.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 232 248 -
9 g11746.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 249 259 -
22 g11746.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 260 283 -
16 g11746.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 284 294 -
19 g11746.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 295 312 -
11 g11746.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 313 317 -
7 g11746.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 72 -
6 g11746.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 85 102 -
5 g11746.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 122 144 -
4 g11746.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -
3 g11746.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 231 248 -
8 g11746.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 261 283 -

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