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.t25 TTS g12311.t25 22334748 22334748
chr_1 g12311 g12311.t25 isoform g12311.t25 22334879 22336083
chr_1 g12311 g12311.t25 exon g12311.t25.exon1 22334879 22335015
chr_1 g12311 g12311.t25 cds g12311.t25.CDS1 22334879 22335015
chr_1 g12311 g12311.t25 exon g12311.t25.exon2 22335076 22335268
chr_1 g12311 g12311.t25 cds g12311.t25.CDS2 22335076 22335268
chr_1 g12311 g12311.t25 exon g12311.t25.exon3 22335329 22335611
chr_1 g12311 g12311.t25 cds g12311.t25.CDS3 22335329 22335565
chr_1 g12311 g12311.t25 exon g12311.t25.exon4 22336010 22336083
chr_1 g12311 g12311.t25 TSS g12311.t25 22336088 22336088

Sequences

>g12311.t25 Gene=g12311 Length=687
GAACGAAAAAAGGTAATTTTTCTGCATTTGCTTTTCTGTCTTTTTTGGATTTTGTGTTTT
AAATAATTGGTTTTATCATTTTAGGCTGTTAAGGGAATAAAAAATCCACATACTTTAAAA
ATGGCGAGTCGAATGATGGCATTGGCTTTACGTCATCAACCAGCCGCTTCAAAGACATCT
TTGATTGTTCGTGCAGCTCACTCAGGCTCAGTGAACCCTCATCTTGCTGAAAAATTAGAG
AAGCTTGGTAATCGCGATGTTGTCGGTTTCGGATGGAACGGAGAACCAACTTACTACGAT
AGGCCAGATTTTCCCATGCCTGCCATTCGTTTTAAGGAAAACACTCCAGATGTTTTGGCT
CTTAGAGCAAAGGAAAAGGAGGACTGGAAGAAGCTGTCGATTCAAGAAAAGAAAGCCCTC
TATCGTGCATCATTCTGTCAGACATTCGCTGAAATGAAATATCCAACAGGAGAATGGAAA
ATGCACTTGGGTAACACACTTATTGTTTTCGCATTAGCAATCTACATTTCACTGTGGATG
GCTGCCTATATCTACGATCCAGATCCCATTTCATTTGATGAAGAACACCAAAAAGCTCAA
CTTAAACGTATGCTTACATTGGAAGTCAATCCTATTCATGGTCTCTCAGCCAATTGGGAC
TATGAAAACAAGAGATGGAAGAAGTAA

>g12311.t25 Gene=g12311 Length=188
MASRMMALALRHQPAASKTSLIVRAAHSGSVNPHLAEKLEKLGNRDVVGFGWNGEPTYYD
RPDFPMPAIRFKENTPDVLALRAKEKEDWKKLSIQEKKALYRASFCQTFAEMKYPTGEWK
MHLGNTLIVFALAIYISLWMAAYIYDPDPISFDEEHQKAQLKRMLTLEVNPIHGLSANWD
YENKRWKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g12311.t25 CDD cd00922 Cyt_c_Oxidase_IV 46 181 1.11272E-64
9 g12311.t25 Gene3D G3DSA:1.10.442.10 Cytochrome C Oxidase 46 188 4.2E-59
2 g12311.t25 PANTHER PTHR10707 CYTOCHROME C OXIDASE SUBUNIT IV 5 188 7.8E-47
6 g12311.t25 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 59 72 3.6E-21
4 g12311.t25 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 102 120 3.6E-21
5 g12311.t25 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 143 156 3.6E-21
3 g12311.t25 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 171 187 3.6E-21
1 g12311.t25 Pfam PF02936 Cytochrome c oxidase subunit IV 51 187 2.7E-52
10 g12311.t25 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 122 -
12 g12311.t25 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 123 145 -
11 g12311.t25 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 146 188 -
7 g12311.t25 SUPERFAMILY SSF81406 Mitochondrial cytochrome c oxidase subunit IV 46 188 7.45E-57
8 g12311.t25 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 17 -
14 g12311.t25 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 123 145 -

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

Pathway

  • This transcript belongs to the following pathways

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