General information for g12311.t21
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cytochrome c oxidase subunit 4 isoform 2, mitochondrial.
Parent gene
- The parent gene g12311 is located on chr_1: 22334879..22343340 (- strand)
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.t21 | TTS | g12311.t21 | 22334748 | 22334748 |
| chr_1 | g12311 | g12311.t21 | isoform | g12311.t21 | 22334879 | 22336073 |
| chr_1 | g12311 | g12311.t21 | exon | g12311.t21.exon1 | 22334879 | 22335015 |
| chr_1 | g12311 | g12311.t21 | cds | g12311.t21.CDS1 | 22334879 | 22335015 |
| chr_1 | g12311 | g12311.t21 | exon | g12311.t21.exon2 | 22335076 | 22335268 |
| chr_1 | g12311 | g12311.t21 | cds | g12311.t21.CDS2 | 22335076 | 22335268 |
| chr_1 | g12311 | g12311.t21 | exon | g12311.t21.exon3 | 22335335 | 22335611 |
| chr_1 | g12311 | g12311.t21 | cds | g12311.t21.CDS3 | 22335335 | 22335565 |
| chr_1 | g12311 | g12311.t21 | exon | g12311.t21.exon4 | 22336010 | 22336073 |
| chr_1 | g12311 | g12311.t21 | TSS | g12311.t21 | 22336088 | 22336088 |
Sequences
>g12311.t21 Gene=g12311 Length=671
AGGTAATTTTTCTGCATTTGCTTTTCTGTCTTTTTTGGATTTTGTGTTTTAAATAATTGG
TTTTATCATTTTAGGCTGTTAAGGGAATAAAAAATCCACATACTTTAAAAATGGCGAGTC
GAATGATGGCATTGGCTTTACGTCATCAACCAGCCGCTTCAAAGACATCTTTGATTGTTC
GTGCAGCTCACTCAGGCTCAGTGAACCCTCATCTTGCTGAAAAATTAGAGAAGCTTGGTA
ATCGCGATGTTGTCGGTTTCGGATGGAACGGAGAACCAACTTACTACGATAGGCCAGATT
TTCCCATGCCTGCCATTCGTTTTAAGGAAAACACTCCAGATGCTCTTAGAGCAAAGGAAA
AGGAGGACTGGAAGAAGCTGTCGATTCAAGAAAAGAAAGCCCTCTATCGTGCATCATTCT
GTCAGACATTCGCTGAAATGAAATATCCAACAGGAGAATGGAAAATGCACTTGGGTAACA
CACTTATTGTTTTCGCATTAGCAATCTACATTTCACTGTGGATGGCTGCCTATATCTACG
ATCCAGATCCCATTTCATTTGATGAAGAACACCAAAAAGCTCAACTTAAACGTATGCTTA
CATTGGAAGTCAATCCTATTCATGGTCTCTCAGCCAATTGGGACTATGAAAACAAGAGAT
GGAAGAAGTAA
>g12311.t21 Gene=g12311 Length=186
MASRMMALALRHQPAASKTSLIVRAAHSGSVNPHLAEKLEKLGNRDVVGFGWNGEPTYYD
RPDFPMPAIRFKENTPDALRAKEKEDWKKLSIQEKKALYRASFCQTFAEMKYPTGEWKMH
LGNTLIVFALAIYISLWMAAYIYDPDPISFDEEHQKAQLKRMLTLEVNPIHGLSANWDYE
NKRWKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g12311.t21 | CDD | cd00922 | Cyt_c_Oxidase_IV | 46 | 179 | 5.41874E-63 |
| 9 | g12311.t21 | Gene3D | G3DSA:1.10.442.10 | Cytochrome C Oxidase | 46 | 186 | 8.3E-58 |
| 2 | g12311.t21 | PANTHER | PTHR10707 | CYTOCHROME C OXIDASE SUBUNIT IV | 5 | 186 | 1.3E-45 |
| 6 | g12311.t21 | PRINTS | PR01873 | Cytochrome c oxidase subunit IV signature | 59 | 72 | 3.4E-21 |
| 5 | g12311.t21 | PRINTS | PR01873 | Cytochrome c oxidase subunit IV signature | 100 | 118 | 3.4E-21 |
| 4 | g12311.t21 | PRINTS | PR01873 | Cytochrome c oxidase subunit IV signature | 141 | 154 | 3.4E-21 |
| 3 | g12311.t21 | PRINTS | PR01873 | Cytochrome c oxidase subunit IV signature | 169 | 185 | 3.4E-21 |
| 1 | g12311.t21 | Pfam | PF02936 | Cytochrome c oxidase subunit IV | 51 | 185 | 9.0E-50 |
| 10 | g12311.t21 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 120 | - |
| 12 | g12311.t21 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 121 | 143 | - |
| 11 | g12311.t21 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 144 | 186 | - |
| 7 | g12311.t21 | SUPERFAMILY | SSF81406 | Mitochondrial cytochrome c oxidase subunit IV | 46 | 186 | 1.96E-54 |
| 8 | g12311.t21 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 17 | - |
| 14 | g12311.t21 | 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 transcript has been annotated with K02263 (cytochrome c oxidase subunit 4)
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. There were no conditions that were differentially expressed