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.t16 TTS g12311.t16 22334748 22334748
chr_1 g12311 g12311.t16 isoform g12311.t16 22334879 22335593
chr_1 g12311 g12311.t16 exon g12311.t16.exon1 22334879 22334970
chr_1 g12311 g12311.t16 cds g12311.t16.CDS1 22334879 22334970
chr_1 g12311 g12311.t16 exon g12311.t16.exon2 22335076 22335268
chr_1 g12311 g12311.t16 cds g12311.t16.CDS2 22335076 22335268
chr_1 g12311 g12311.t16 exon g12311.t16.exon3 22335329 22335593
chr_1 g12311 g12311.t16 cds g12311.t16.CDS3 22335329 22335565
chr_1 g12311 g12311.t16 TSS g12311.t16 22336088 22336088

Sequences

>g12311.t16 Gene=g12311 Length=550
GGGAATAAAAAATCCACATACTTTAAAAATGGCGAGTCGAATGATGGCATTGGCTTTACG
TCATCAACCAGCCGCTTCAAAGACATCTTTGATTGTTCGTGCAGCTCACTCAGGCTCAGT
GAACCCTCATCTTGCTGAAAAATTAGAGAAGCTTGGTAATCGCGATGTTGTCGGTTTCGG
ATGGAACGGAGAACCAACTTACTACGATAGGCCAGATTTTCCCATGCCTGCCATTCGTTT
TAAGGAAAACACTCCAGATGTTTTGGCTCTTAGAGCAAAGGAAAAGGAGGACTGGAAGAA
GCTGTCGATTCAAGAAAAGAAAGCCCTCTATCGTGCATCATTCTGTCAGACATTCGCTGA
AATGAAATATCCAACAGGAGAATGGAAAATGCACTTGGGTAACACACTTATTGTTTTCGC
ATTAGCAATCTACATTTCACTGTGGATGGCTGCCTATACTCAACTTAAACGTATGCTTAC
ATTGGAAGTCAATCCTATTCATGGTCTCTCAGCCAATTGGGACTATGAAAACAAGAGATG
GAAGAAGTAA

>g12311.t16 Gene=g12311 Length=173
MASRMMALALRHQPAASKTSLIVRAAHSGSVNPHLAEKLEKLGNRDVVGFGWNGEPTYYD
RPDFPMPAIRFKENTPDVLALRAKEKEDWKKLSIQEKKALYRASFCQTFAEMKYPTGEWK
MHLGNTLIVFALAIYISLWMAAYTQLKRMLTLEVNPIHGLSANWDYENKRWKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g12311.t16 CDD cd00922 Cyt_c_Oxidase_IV 46 166 4.48976E-54
7 g12311.t16 Gene3D G3DSA:1.10.442.10 Cytochrome C Oxidase 46 173 5.7E-46
2 g12311.t16 PANTHER PTHR10707 CYTOCHROME C OXIDASE SUBUNIT IV 5 173 6.0E-36
4 g12311.t16 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 59 72 8.1E-8
3 g12311.t16 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 102 120 8.1E-8
1 g12311.t16 Pfam PF02936 Cytochrome c oxidase subunit IV 51 172 3.2E-39
8 g12311.t16 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 121 -
10 g12311.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 142 -
9 g12311.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 173 -
5 g12311.t16 SUPERFAMILY SSF81406 Mitochondrial cytochrome c oxidase subunit IV 46 173 2.75E-47
6 g12311.t16 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 17 -
12 g12311.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 121 143 -

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