General information for g9658.t78
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable 28S ribosomal protein S6, mitochondrial.
Parent gene
- The parent gene g9658 is located on chr_1: 4507179..4507788 (- 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 | g9658 | g9658.t78 | TTS | g9658.t78 | 4507106 | 4507106 |
| chr_1 | g9658 | g9658.t78 | isoform | g9658.t78 | 4507179 | 4507788 |
| chr_1 | g9658 | g9658.t78 | exon | g9658.t78.exon1 | 4507179 | 4507432 |
| chr_1 | g9658 | g9658.t78 | cds | g9658.t78.CDS1 | 4507179 | 4507432 |
| chr_1 | g9658 | g9658.t78 | exon | g9658.t78.exon2 | 4507493 | 4507630 |
| chr_1 | g9658 | g9658.t78 | cds | g9658.t78.CDS2 | 4507493 | 4507630 |
| chr_1 | g9658 | g9658.t78 | exon | g9658.t78.exon3 | 4507740 | 4507788 |
| chr_1 | g9658 | g9658.t78 | cds | g9658.t78.CDS3 | 4507740 | 4507788 |
| chr_1 | g9658 | g9658.t78 | TSS | g9658.t78 | 4507861 | 4507861 |
Sequences
>g9658.t78 Gene=g9658 Length=441
ATGCCGACATATGAACTAGCACTTATGTTGAGAACAATGTCAAGAGTAATAACTACACTT
AAAAGAACAACAGAAGCGATTTTCTCAAAAGGCGGTTTTCTAAGACAACTCGATTATTTG
GGTGATAAACAGTTACCATATAGAGTTCACAAAAATTCACAGAAACATTTTACTGGATCA
GCATTTATTGTTACATTTGATGTATCACCGAAAAAATTGGATGATCTGTTAGAAGAATAT
ACTCGAGATGTTGACATACTTAAACGTTCAATTTTTAAAATAGAAGATGAGCCACAAAAA
ATTGAATGCACCCTTGATGAAGAATTAAAACCACCAGCATATAGGAAAGAGGTCATTAAT
ATGATGGAAAAGGCAGCAAAAGGTCAAAAAGAAAAATATCCACAAAATACAGGATTAAAT
TACTATCCTTTCCAAAAATAA
>g9658.t78 Gene=g9658 Length=146
MPTYELALMLRTMSRVITTLKRTTEAIFSKGGFLRQLDYLGDKQLPYRVHKNSQKHFTGS
AFIVTFDVSPKKLDDLLEEYTRDVDILKRSIFKIEDEPQKIECTLDEELKPPAYRKEVIN
MMEKAAKGQKEKYPQNTGLNYYPFQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9658.t78 | CDD | cd15465 | bS6_mito | 3 | 94 | 6.23432E-29 |
| 5 | g9658.t78 | Coils | Coil | Coil | 77 | 97 | - |
| 4 | g9658.t78 | Gene3D | G3DSA:3.30.70.60 | - | 1 | 125 | 3.0E-23 |
| 2 | g9658.t78 | PANTHER | PTHR21011 | MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S6 | 1 | 104 | 5.0E-16 |
| 1 | g9658.t78 | Pfam | PF01250 | Ribosomal protein S6 | 4 | 93 | 3.6E-13 |
| 3 | g9658.t78 | SUPERFAMILY | SSF54995 | Ribosomal protein S6 | 1 | 97 | 3.14E-14 |
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:0005840 | ribosome | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
| GO:0019843 | rRNA binding | 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