General information for g9658.t1
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.t1 | TTS | g9658.t1 | 4507106 | 4507106 |
| chr_1 | g9658 | g9658.t1 | isoform | g9658.t1 | 4507179 | 4507788 |
| chr_1 | g9658 | g9658.t1 | exon | g9658.t1.exon1 | 4507179 | 4507432 |
| chr_1 | g9658 | g9658.t1 | cds | g9658.t1.CDS1 | 4507179 | 4507432 |
| chr_1 | g9658 | g9658.t1 | exon | g9658.t1.exon2 | 4507493 | 4507640 |
| chr_1 | g9658 | g9658.t1 | cds | g9658.t1.CDS2 | 4507493 | 4507640 |
| chr_1 | g9658 | g9658.t1 | exon | g9658.t1.exon3 | 4507744 | 4507788 |
| chr_1 | g9658 | g9658.t1 | cds | g9658.t1.CDS3 | 4507744 | 4507788 |
| chr_1 | g9658 | g9658.t1 | TSS | g9658.t1 | 4507861 | 4507861 |
Sequences
>g9658.t1 Gene=g9658 Length=447
ATGCCGACATATGAACTAGCACTTATGTTGAGAACAATGTCAAGACCTGAAATAGTAACT
ACACTTAAAAGAACAACAGAAGCGATTTTCTCAAAAGGCGGTTTTCTAAGACAACTCGAT
TATTTGGGTGATAAACAGTTACCATATAGAGTTCACAAAAATTCACAGAAACATTTTACT
GGATCAGCATTTATTGTTACATTTGATGTATCACCGAAAAAATTGGATGATCTGTTAGAA
GAATATACTCGAGATGTTGACATACTTAAACGTTCAATTTTTAAAATAGAAGATGAGCCA
CAAAAAATTGAATGCACCCTTGATGAAGAATTAAAACCACCAGCATATAGGAAAGAGGTC
ATTAATATGATGGAAAAGGCAGCAAAAGGTCAAAAAGAAAAATATCCACAAAATACAGGA
TTAAATTACTATCCTTTCCAAAAATAA
>g9658.t1 Gene=g9658 Length=148
MPTYELALMLRTMSRPEIVTTLKRTTEAIFSKGGFLRQLDYLGDKQLPYRVHKNSQKHFT
GSAFIVTFDVSPKKLDDLLEEYTRDVDILKRSIFKIEDEPQKIECTLDEELKPPAYRKEV
INMMEKAAKGQKEKYPQNTGLNYYPFQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9658.t1 | CDD | cd15465 | bS6_mito | 3 | 96 | 4.49474E-32 |
| 5 | g9658.t1 | Coils | Coil | Coil | 79 | 99 | - |
| 4 | g9658.t1 | Gene3D | G3DSA:3.30.70.60 | - | 1 | 127 | 7.8E-27 |
| 2 | g9658.t1 | PANTHER | PTHR21011 | MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S6 | 1 | 106 | 3.5E-19 |
| 1 | g9658.t1 | Pfam | PF01250 | Ribosomal protein S6 | 4 | 95 | 1.4E-14 |
| 3 | g9658.t1 | SUPERFAMILY | SSF54995 | Ribosomal protein S6 | 1 | 99 | 8.11E-17 |
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 transcript has been annotated with K02990 (small subunit ribosomal protein S6)
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.
