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.t6 TTS g12311.t6 22334748 22334748
chr_1 g12311 g12311.t6 isoform g12311.t6 22334749 22335611
chr_1 g12311 g12311.t6 exon g12311.t6.exon1 22334749 22335015
chr_1 g12311 g12311.t6 cds g12311.t6.CDS1 22334879 22335015
chr_1 g12311 g12311.t6 exon g12311.t6.exon2 22335076 22335247
chr_1 g12311 g12311.t6 cds g12311.t6.CDS2 22335076 22335247
chr_1 g12311 g12311.t6 exon g12311.t6.exon3 22335329 22335611
chr_1 g12311 g12311.t6 cds g12311.t6.CDS3 22335329 22335565
chr_1 g12311 g12311.t6 TSS g12311.t6 22336088 22336088

Sequences

>g12311.t6 Gene=g12311 Length=722
ATCATTTTAGGCTGTTAAGGGAATAAAAAATCCACATACTTTAAAAATGGCGAGTCGAAT
GATGGCATTGGCTTTACGTCATCAACCAGCCGCTTCAAAGACATCTTTGATTGTTCGTGC
AGCTCACTCAGGCTCAGTGAACCCTCATCTTGCTGAAAAATTAGAGAAGCTTGGTAATCG
CGATGTTGTCGGTTTCGGATGGAACGGAGAACCAACTTACTACGATAGGCCAGATTTTCC
CATGCCTGCCATTCGTTTTAAGGAAAACACTCCAGATGTTTTGGAGGACTGGAAGAAGCT
GTCGATTCAAGAAAAGAAAGCCCTCTATCGTGCATCATTCTGTCAGACATTCGCTGAAAT
GAAATATCCAACAGGAGAATGGAAAATGCACTTGGGTAACACACTTATTGTTTTCGCATT
AGCAATCTACATTTCACTGTGGATGGCTGCCTATATCTACGATCCAGATCCCATTTCATT
TGATGAAGAACACCAAAAAGCTCAACTTAAACGTATGCTTACATTGGAAGTCAATCCTAT
TCATGGTCTCTCAGCCAATTGGGACTATGAAAACAAGAGATGGAAGAAGTAAATTTCCGA
CACTTGAAGACAGTGGTGTCCAATTTTCCTAAAGAAAAATAGAAGTTATTATTTTCGATT
GTTCATTCAATTGAACTACAAAATTCAACAGAAAAAAATGTCAAATAAATGTATAAAACT
AA

>g12311.t6 Gene=g12311 Length=181
MASRMMALALRHQPAASKTSLIVRAAHSGSVNPHLAEKLEKLGNRDVVGFGWNGEPTYYD
RPDFPMPAIRFKENTPDVLEDWKKLSIQEKKALYRASFCQTFAEMKYPTGEWKMHLGNTL
IVFALAIYISLWMAAYIYDPDPISFDEEHQKAQLKRMLTLEVNPIHGLSANWDYENKRWK
K

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g12311.t6 CDD cd00922 Cyt_c_Oxidase_IV 46 174 1.37706E-57
8 g12311.t6 Gene3D G3DSA:1.10.442.10 Cytochrome C Oxidase 46 181 1.1E-51
2 g12311.t6 PANTHER PTHR10707 CYTOCHROME C OXIDASE SUBUNIT IV 5 181 3.5E-39
5 g12311.t6 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 59 72 1.1E-13
3 g12311.t6 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 136 149 1.1E-13
4 g12311.t6 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 164 180 1.1E-13
1 g12311.t6 Pfam PF02936 Cytochrome c oxidase subunit IV 51 180 1.6E-43
9 g12311.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 115 -
11 g12311.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 138 -
10 g12311.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 139 181 -
6 g12311.t6 SUPERFAMILY SSF81406 Mitochondrial cytochrome c oxidase subunit IV 46 181 2.09E-50
7 g12311.t6 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 17 -
13 g12311.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 116 138 -

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