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.t20 TTS g12311.t20 22334748 22334748
chr_1 g12311 g12311.t20 isoform g12311.t20 22334879 22336063
chr_1 g12311 g12311.t20 exon g12311.t20.exon1 22334879 22335268
chr_1 g12311 g12311.t20 cds g12311.t20.CDS1 22334879 22335268
chr_1 g12311 g12311.t20 exon g12311.t20.exon2 22335329 22335611
chr_1 g12311 g12311.t20 cds g12311.t20.CDS2 22335329 22335565
chr_1 g12311 g12311.t20 exon g12311.t20.exon3 22336010 22336063
chr_1 g12311 g12311.t20 TSS g12311.t20 22336088 22336088

Sequences

>g12311.t20 Gene=g12311 Length=727
TCTGCATTTGCTTTTCTGTCTTTTTTGGATTTTGTGTTTTAAATAATTGGTTTTATCATT
TTAGGCTGTTAAGGGAATAAAAAATCCACATACTTTAAAAATGGCGAGTCGAATGATGGC
ATTGGCTTTACGTCATCAACCAGCCGCTTCAAAGACATCTTTGATTGTTCGTGCAGCTCA
CTCAGGCTCAGTGAACCCTCATCTTGCTGAAAAATTAGAGAAGCTTGGTAATCGCGATGT
TGTCGGTTTCGGATGGAACGGAGAACCAACTTACTACGATAGGCCAGATTTTCCCATGCC
TGCCATTCGTTTTAAGGAAAACACTCCAGATGTTTTGGCTCTTAGAGCAAAGGAAAAGGA
GGACTGGAAGAAGCTGTCGATTCAAGAAAAGAAAGCCCTCTATCGTGCATCATTCTGTCA
GACATTCGCTGAAATGAAATATCCAACAGGAGAATGGAAAATGCACTTGGGTAACACACT
TATTGTTTTCGCATTAGCAATCTACATTTCACTGTGGATGGCTGCCTATAGTAAGTTATC
AAAACAAAATATATATATGGTCATAAATAAACATTTTAATTTTTCTTTAGTCTACGATCC
AGATCCCATTTCATTTGATGAAGAACACCAAAAAGCTCAACTTAAACGTATGCTTACATT
GGAAGTCAATCCTATTCATGGTCTCTCAGCCAATTGGGACTATGAAAACAAGAGATGGAA
GAAGTAA

>g12311.t20 Gene=g12311 Length=208
MASRMMALALRHQPAASKTSLIVRAAHSGSVNPHLAEKLEKLGNRDVVGFGWNGEPTYYD
RPDFPMPAIRFKENTPDVLALRAKEKEDWKKLSIQEKKALYRASFCQTFAEMKYPTGEWK
MHLGNTLIVFALAIYISLWMAAYSKLSKQNIYMVINKHFNFSLVYDPDPISFDEEHQKAQ
LKRMLTLEVNPIHGLSANWDYENKRWKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g12311.t20 CDD cd00922 Cyt_c_Oxidase_IV 46 201 6.19592E-61
8 g12311.t20 Gene3D G3DSA:1.10.442.10 Cytochrome C Oxidase 46 157 5.4E-36
3 g12311.t20 PANTHER PTHR10707 CYTOCHROME C OXIDASE SUBUNIT IV 5 208 1.8E-43
5 g12311.t20 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 59 72 1.1E-7
4 g12311.t20 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 102 120 1.1E-7
2 g12311.t20 Pfam PF02936 Cytochrome c oxidase subunit IV 51 143 5.8E-31
1 g12311.t20 Pfam PF02936 Cytochrome c oxidase subunit IV 162 207 3.6E-14
10 g12311.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 121 -
11 g12311.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 143 -
9 g12311.t20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 144 208 -
6 g12311.t20 SUPERFAMILY SSF81406 Mitochondrial cytochrome c oxidase subunit IV 46 208 7.59E-51
7 g12311.t20 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 17 -
13 g12311.t20 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.

Raw TPM values