Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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.t23 TTS g12311.t23 22334748 22334748
chr_1 g12311 g12311.t23 isoform g12311.t23 22334879 22336077
chr_1 g12311 g12311.t23 exon g12311.t23.exon1 22334879 22335015
chr_1 g12311 g12311.t23 cds g12311.t23.CDS1 22334988 22335015
chr_1 g12311 g12311.t23 exon g12311.t23.exon2 22335072 22335268
chr_1 g12311 g12311.t23 cds g12311.t23.CDS2 22335072 22335268
chr_1 g12311 g12311.t23 exon g12311.t23.exon3 22335329 22335576
chr_1 g12311 g12311.t23 cds g12311.t23.CDS3 22335329 22335565
chr_1 g12311 g12311.t23 exon g12311.t23.exon4 22336010 22336077
chr_1 g12311 g12311.t23 TSS g12311.t23 22336088 22336088

Sequences

>g12311.t23 Gene=g12311 Length=650
AAAAAGGTAATTTTTCTGCATTTGCTTTTCTGTCTTTTTTGGATTTTGTGTTTTAAATAA
TTGGTTTTATACTTTAAAAATGGCGAGTCGAATGATGGCATTGGCTTTACGTCATCAACC
AGCCGCTTCAAAGACATCTTTGATTGTTCGTGCAGCTCACTCAGGCTCAGTGAACCCTCA
TCTTGCTGAAAAATTAGAGAAGCTTGGTAATCGCGATGTTGTCGGTTTCGGATGGAACGG
AGAACCAACTTACTACGATAGGCCAGATTTTCCCATGCCTGCCATTCGTTTTAAGGAAAA
CACTCCAGATGTTTTGGCTCTTAGAGCAAAGGAAAAGGAGGACTGGAAGAAGCTGTCGAT
TCAAGAAAAGAAAGCCCTCTATCGTGCATCATTCTGTCAGACATTCGCTGAAATGAAATA
TCCAACAGGAGAATGGAAAATGCACTTGGGTAACACACTTATTGTTTTCGCATTAGCAAT
CTACATTTCACTGTGGATGGCTGCCTATAGTAATCTACGATCCAGATCCCATTTCATTTG
ATGAAGAACACCAAAAAGCTCAACTTAAACGTATGCTTACATTGGAAGTCAATCCTATTC
ATGGTCTCTCAGCCAATTGGGACTATGAAAACAAGAGATGGAAGAAGTAA

>g12311.t23 Gene=g12311 Length=153
MASRMMALALRHQPAASKTSLIVRAAHSGSVNPHLAEKLEKLGNRDVVGFGWNGEPTYYD
RPDFPMPAIRFKENTPDVLALRAKEKEDWKKLSIQEKKALYRASFCQTFAEMKYPTGEWK
MHLGNTLIVFALAIYISLWMAAYSNLRSRSHFI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g12311.t23 CDD cd00922 Cyt_c_Oxidase_IV 46 145 2.79888E-46
8 g12311.t23 Gene3D G3DSA:1.10.442.10 Cytochrome C Oxidase 46 152 1.6E-36
2 g12311.t23 PANTHER PTHR10707 CYTOCHROME C OXIDASE SUBUNIT IV 4 144 5.0E-29
3 g12311.t23 PANTHER PTHR10707:SF10 AT07685P-RELATED 4 144 5.0E-29
5 g12311.t23 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 59 72 6.8E-8
4 g12311.t23 PRINTS PR01873 Cytochrome c oxidase subunit IV signature 102 120 6.8E-8
1 g12311.t23 Pfam PF02936 Cytochrome c oxidase subunit IV 51 143 2.4E-31
9 g12311.t23 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 121 -
11 g12311.t23 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 142 -
10 g12311.t23 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 153 -
6 g12311.t23 SUPERFAMILY SSF81406 Mitochondrial cytochrome c oxidase subunit IV 46 143 1.28E-35
7 g12311.t23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 17 -
13 g12311.t23 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