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.t7 TTS g12311.t7 22334748 22334748
chr_1 g12311 g12311.t7 isoform g12311.t7 22334749 22336063
chr_1 g12311 g12311.t7 exon g12311.t7.exon1 22334749 22335003
chr_1 g12311 g12311.t7 cds g12311.t7.CDS1 22334879 22335003
chr_1 g12311 g12311.t7 exon g12311.t7.exon2 22335076 22335268
chr_1 g12311 g12311.t7 cds g12311.t7.CDS2 22335076 22335268
chr_1 g12311 g12311.t7 exon g12311.t7.exon3 22335329 22335611
chr_1 g12311 g12311.t7 cds g12311.t7.CDS3 22335329 22335565
chr_1 g12311 g12311.t7 exon g12311.t7.exon4 22336010 22336063
chr_1 g12311 g12311.t7 TSS g12311.t7 22336088 22336088

Sequences

>g12311.t7 Gene=g12311 Length=785
TCTGCATTTGCTTTTCTGTCTTTTTTGGATTTTGTGTTTTAAATAATTGGTTTTATCATT
TTAGGCTGTTAAGGGAATAAAAAATCCACATACTTTAAAAATGGCGAGTCGAATGATGGC
ATTGGCTTTACGTCATCAACCAGCCGCTTCAAAGACATCTTTGATTGTTCGTGCAGCTCA
CTCAGGCTCAGTGAACCCTCATCTTGCTGAAAAATTAGAGAAGCTTGGTAATCGCGATGT
TGTCGGTTTCGGATGGAACGGAGAACCAACTTACTACGATAGGCCAGATTTTCCCATGCC
TGCCATTCGTTTTAAGGAAAACACTCCAGATGTTTTGGCTCTTAGAGCAAAGGAAAAGGA
GGACTGGAAGAAGCTGTCGATTCAAGAAAAGAAAGCCCTCTATCGTGCATCATTCTGTCA
GACATTCGCTGAAATGAAATATCCAACAGGAGAATGGAAAATGCACTTGGGTAACACACT
TATTGTTTTCGCATTAGCAATCTACATTTCACTGTGGATGGCTGCCTATAATCCCATTTC
ATTTGATGAAGAACACCAAAAAGCTCAACTTAAACGTATGCTTACATTGGAAGTCAATCC
TATTCATGGTCTCTCAGCCAATTGGGACTATGAAAACAAGAGATGGAAGAAGTAAATTTC
CGACACTTGAAGACAGTGGTGTCCAATTTTCCTAAAGAAAAATAGAAGTTATTATTTTCG
ATTGTTCATTCAATTGAACTACAAAATTCAACAGAAAAAAATGTCAAATAAATGTATAAA
ACTAA

>g12311.t7 Gene=g12311 Length=184
MASRMMALALRHQPAASKTSLIVRAAHSGSVNPHLAEKLEKLGNRDVVGFGWNGEPTYYD
RPDFPMPAIRFKENTPDVLALRAKEKEDWKKLSIQEKKALYRASFCQTFAEMKYPTGEWK
MHLGNTLIVFALAIYISLWMAAYNPISFDEEHQKAQLKRMLTLEVNPIHGLSANWDYENK
RWKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g12311.t7 CDD cd00922 Cyt_c_Oxidase_IV 46 177 2.16638E-61
8 g12311.t7 Gene3D G3DSA:1.10.442.10 Cytochrome C Oxidase 46 184 1.2E-54
2 g12311.t7 PANTHER PTHR10707 CYTOCHROME C OXIDASE SUBUNIT IV 5 184 1.4E-42
4 g12311.t7 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 59 72 1.5E-15
3 g12311.t7 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 102 120 1.5E-15
5 g12311.t7 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 167 183 1.5E-15
1 g12311.t7 Pfam PF02936 Cytochrome c oxidase subunit IV 51 183 2.9E-48
9 g12311.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 121 -
11 g12311.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 142 -
10 g12311.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 184 -
6 g12311.t7 SUPERFAMILY SSF81406 Mitochondrial cytochrome c oxidase subunit IV 46 184 3.01E-53
7 g12311.t7 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 17 -
13 g12311.t7 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