General information for g13857.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cytochrome c oxidase subunit 5B, mitochondrial.
Parent gene
- The parent gene g13857 is located on chr_1: 32864604..32866817 (+ 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 | g13857 | g13857.t13 | TSS | g13857.t13 | 32864176 | 32864176 |
| chr_1 | g13857 | g13857.t13 | isoform | g13857.t13 | 32864251 | 32866817 |
| chr_1 | g13857 | g13857.t13 | exon | g13857.t13.exon1 | 32864251 | 32864329 |
| chr_1 | g13857 | g13857.t13 | cds | g13857.t13.CDS1 | 32864251 | 32864329 |
| chr_1 | g13857 | g13857.t13 | exon | g13857.t13.exon2 | 32864604 | 32864777 |
| chr_1 | g13857 | g13857.t13 | cds | g13857.t13.CDS2 | 32864604 | 32864777 |
| chr_1 | g13857 | g13857.t13 | exon | g13857.t13.exon3 | 32864837 | 32865197 |
| chr_1 | g13857 | g13857.t13 | cds | g13857.t13.CDS3 | 32864837 | 32864943 |
| chr_1 | g13857 | g13857.t13 | exon | g13857.t13.exon4 | 32866538 | 32866817 |
| chr_1 | g13857 | g13857.t13 | TTS | g13857.t13 | NA | NA |
Sequences
>g13857.t13 Gene=g13857 Length=894
ATGGCGTCTTTGACTGGTCGCATTGTGCTCGCAGCAGCTCGTAGAAATGTACAATACACT
CCAGTTCGTTTCTGCAAAATGATGAACGATCCATTGGAACACGCAACTGGTCTTGAAAAA
CGCGAGTTGCTTGCTAAAGCTGCCGGCAATGATAATCCATTCGACATGAAAGTATTTAAA
CGCGGTCCAGGCACTAAAGAAAACCCAAATTTAATTCCATCAGCTTTCGATGCTCGTTTG
GTCGGTTGTATATGTGAGGAAGAACAGACATACGTTAATTGGATGTGGCTCTATCAAGGA
CATCCAAAGAGATGCGAATGTGGTCACTGGTTCAAATTAGTCGAAAAGGCTCCAGTATAA
ATCACTAACCGCCAGCAACTACCTTCAAATCTTCAATTTTACATCCACACTTAAAGAAAA
TATTATAGTTTTTCGTGTTAAAGATTCCAAACTTAAAAGAGAGATGTGGAACATTTCCCC
AAAAAGAGATCAAGAAGCAGAAAAGTTAAATTCGTGGAAAATTATATTTGAGGGAAAATA
AAAATTTGTGAATTAGTCAAAAAAACTAAATTGAAGGCAGTTGTCATTTATAAAATTAGA
GACATTTAGTTTTATTAAATGCAAAAATCTTTTTTTTTTCCTTTCACTCAACTCGTCATT
TTTTCTCTTACTCGTCGTTCGCCTTTTTTGCTTTATTTAACAGGTTCCCGAATAAAAATA
AAATACACACTTGAGAGGAGGTGAGGAGGTACAGAGTCGCAGACAATGCAGATATATGAA
ATAGTAAAAATCAAAAAAAACTTTCACTCAAAGTAGGTCACTTAAGAAGAAGTCACTTAT
CACTTATCAGACAGACACAAAGAATGTACAAAAATATTTTAATGAATATATACC
>g13857.t13 Gene=g13857 Length=119
MASLTGRIVLAAARRNVQYTPVRFCKMMNDPLEHATGLEKRELLAKAAGNDNPFDMKVFK
RGPGTKENPNLIPSAFDARLVGCICEEEQTYVNWMWLYQGHPKRCECGHWFKLVEKAPV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13857.t13 | CDD | cd00924 | Cyt_c_Oxidase_Vb | 24 | 119 | 0.00 |
| 5 | g13857.t13 | Gene3D | G3DSA:2.60.11.10 | Cytochrome C Oxidase | 26 | 118 | 0.00 |
| 2 | g13857.t13 | PANTHER | PTHR10122 | CYTOCHROME C OXIDASE SUBUNIT 5B, MITOCHONDRIAL | 26 | 113 | 0.00 |
| 3 | g13857.t13 | PANTHER | PTHR10122:SF0 | CYTOCHROME C OXIDASE SUBUNIT 5B, MITOCHONDRIAL | 26 | 113 | 0.00 |
| 1 | g13857.t13 | Pfam | PF01215 | Cytochrome c oxidase subunit Vb | 32 | 114 | 0.00 |
| 6 | g13857.t13 | ProSiteProfiles | PS51359 | Cytochrome c oxidase subunit Vb, zinc binding domain profile. | 23 | 119 | 23.38 |
| 4 | g13857.t13 | SUPERFAMILY | SSF57802 | Rubredoxin-like | 25 | 115 | 0.00 |
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:0005740 | mitochondrial envelope | CC |
| GO:0004129 | cytochrome-c oxidase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K02265 (cytochrome c oxidase subunit 5b)
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.
