Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Cytochrome c oxidase subunit 4 isoform 2, mitochondrial.

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 g12311 g12311.t13 TTS g12311.t13 22334748 22334748
chr_1 g12311 g12311.t13 isoform g12311.t13 22334879 22335565
chr_1 g12311 g12311.t13 exon g12311.t13.exon1 22334879 22335015
chr_1 g12311 g12311.t13 cds g12311.t13.CDS1 22334879 22335015
chr_1 g12311 g12311.t13 exon g12311.t13.exon2 22335076 22335260
chr_1 g12311 g12311.t13 cds g12311.t13.CDS2 22335076 22335260
chr_1 g12311 g12311.t13 exon g12311.t13.exon3 22335400 22335565
chr_1 g12311 g12311.t13 cds g12311.t13.CDS3 22335400 22335413
chr_1 g12311 g12311.t13 TSS g12311.t13 22336088 22336088

Sequences

>g12311.t13 Gene=g12311 Length=488
ATGGCGAGTCGAATGATGGCATTGGCTTTACGTCATCAACCAGCCGCTTCAAAGACATCT
TTGATTGTTCGTGCAGCTCACTCAGGCTCAGTGAACCCTCATCTTGCTGAAAAATTAGAG
AAGCTTGGTAATCGCGATGTTGTCGGTTTCGGATGGAACGGAGAACAGCAAAGGAAAAGG
AGGACTGGAAGAAGCTGTCGATTCAAGAAAAGAAAGCCCTCTATCGTGCATCATTCTGTC
AGACATTCGCTGAAATGAAATATCCAACAGGAGAATGGAAAATGCACTTGGGTAACACAC
TTATTGTTTTCGCATTAGCAATCTACATTTCACTGTGGATGGCTGCCTATATCTACGATC
CAGATCCCATTTCATTTGATGAAGAACACCAAAAAGCTCAACTTAAACGTATGCTTACAT
TGGAAGTCAATCCTATTCATGGTCTCTCAGCCAATTGGGACTATGAAAACAAGAGATGGA
AGAAGTAA

>g12311.t13 Gene=g12311 Length=111
MERRTAKEKEDWKKLSIQEKKALYRASFCQTFAEMKYPTGEWKMHLGNTLIVFALAIYIS
LWMAAYIYDPDPISFDEEHQKAQLKRMLTLEVNPIHGLSANWDYENKRWKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g12311.t13 CDD cd00922 Cyt_c_Oxidase_IV 5 104 5.8959E-44
7 g12311.t13 Gene3D G3DSA:1.10.442.10 Cytochrome C Oxidase 2 111 2.3E-46
2 g12311.t13 PANTHER PTHR10707 CYTOCHROME C OXIDASE SUBUNIT IV 6 111 2.9E-37
5 g12311.t13 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 25 43 1.9E-15
3 g12311.t13 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 66 79 1.9E-15
4 g12311.t13 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 94 110 1.9E-15
1 g12311.t13 Pfam PF02936 Cytochrome c oxidase subunit IV 6 110 3.4E-41
8 g12311.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 45 -
10 g12311.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 46 68 -
9 g12311.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 69 111 -
6 g12311.t13 SUPERFAMILY SSF81406 Mitochondrial cytochrome c oxidase subunit IV 6 111 9.42E-43
12 g12311.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 46 68 -

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:0004129 cytochrome-c oxidase activity MF

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. There were no conditions that were differentially expressed