General information for g10508.t26
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 40S ribosomal protein S18.
Parent gene
- The parent gene g10508 is located on chr_1: 10277781..10287560 (+ 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 | g10508 | g10508.t26 | isoform | g10508.t26 | 10276903 | 10278050 |
| chr_1 | g10508 | g10508.t26 | exon | g10508.t26.exon1 | 10276903 | 10277062 |
| chr_1 | g10508 | g10508.t26 | exon | g10508.t26.exon2 | 10277507 | 10277706 |
| chr_1 | g10508 | g10508.t26 | cds | g10508.t26.CDS1 | 10277518 | 10277706 |
| chr_1 | g10508 | g10508.t26 | exon | g10508.t26.exon3 | 10277781 | 10277913 |
| chr_1 | g10508 | g10508.t26 | cds | g10508.t26.CDS2 | 10277781 | 10277913 |
| chr_1 | g10508 | g10508.t26 | exon | g10508.t26.exon4 | 10278016 | 10278050 |
| chr_1 | g10508 | g10508.t26 | cds | g10508.t26.CDS3 | 10278016 | 10278050 |
| chr_1 | g10508 | g10508.t26 | TTS | g10508.t26 | 10278168 | 10278168 |
| chr_1 | g10508 | g10508.t26 | TSS | g10508.t26 | NA | NA |
Sequences
>g10508.t26 Gene=g10508 Length=528
ATGAAATTATTAAAAATAAAAAATTATTGTTTGCCAGAAAATACTTCCGCGCGTCAATAT
GGAAAAAATTTCTTTTCAAAAAGATGCGAAACAACAAATTTTTTGACGCAAAAAGTTGAC
TCTTTCTTTTTCGCATCTTTTATTGAGCAGGCGTGCAAAAAAAATAATAAGATGTCTCTC
GTCATACCTGAGAAGTTTCAACATATTTTGCGTATTATGAGTACCAATATCGATGGTAAA
CGCAAAGTTCCGGTCGCAATGACTGCCATCAAGGGTGTCGGTCGTCGTTACTCACACGTA
GTCCTCAGAAAAGCCGATGTTGATGTTGACAAACGTGCCGGTGAATGTACTGAGGAAGAA
GTCGAAAAAATTGTCACAATTATTTCCAATCCACGTCAATATAAAATTCCAGATTGGTTT
CTTAACAGACAAAAGGATATCATCGATGGTAAATATTCACAATTGACCTCTTCACTCGTC
GATTCAAAATTGCGCGGACGTACTGTTGGTGTGTCAAAGAAGAAGTAA
>g10508.t26 Gene=g10508 Length=118
MSLVIPEKFQHILRIMSTNIDGKRKVPVAMTAIKGVGRRYSHVVLRKADVDVDKRAGECT
EEEVEKIVTIISNPRQYKIPDWFLNRQKDIIDGKYSQLTSSLVDSKLRGRTVGVSKKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10508.t26 | Gene3D | G3DSA:1.10.8.50 | - | 1 | 80 | 0.000 |
| 2 | g10508.t26 | PANTHER | PTHR10871 | 30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18 | 1 | 108 | 0.000 |
| 3 | g10508.t26 | PANTHER | PTHR10871:SF3 | 40S RIBOSOMAL PROTEIN S18-RELATED | 1 | 108 | 0.000 |
| 1 | g10508.t26 | Pfam | PF00416 | Ribosomal protein S13/S18 | 14 | 108 | 0.000 |
| 6 | g10508.t26 | ProSiteProfiles | PS50159 | Ribosomal protein S13 family profile. | 15 | 79 | 17.171 |
| 4 | g10508.t26 | SUPERFAMILY | SSF46946 | S13-like H2TH domain | 13 | 74 | 0.000 |
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:0003723 | RNA binding | MF |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
| GO:0003676 | nucleic acid 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