General information for g10508.t20
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.t20 | isoform | g10508.t20 | 10276903 | 10278050 |
| chr_1 | g10508 | g10508.t20 | exon | g10508.t20.exon1 | 10276903 | 10277062 |
| chr_1 | g10508 | g10508.t20 | cds | g10508.t20.CDS1 | 10276903 | 10277062 |
| chr_1 | g10508 | g10508.t20 | exon | g10508.t20.exon2 | 10277507 | 10277710 |
| chr_1 | g10508 | g10508.t20 | cds | g10508.t20.CDS2 | 10277507 | 10277710 |
| chr_1 | g10508 | g10508.t20 | exon | g10508.t20.exon3 | 10277781 | 10278050 |
| chr_1 | g10508 | g10508.t20 | cds | g10508.t20.CDS3 | 10277781 | 10277824 |
| chr_1 | g10508 | g10508.t20 | TTS | g10508.t20 | 10278168 | 10278168 |
| chr_1 | g10508 | g10508.t20 | TSS | g10508.t20 | NA | NA |
Sequences
>g10508.t20 Gene=g10508 Length=634
ATGAAATTATTAAAAATAAAAAATTATTGTTTGCCAGAAAATACTTCCGCGCGTCAATAT
GGAAAAAATTTCTTTTCAAAAAGATGCGAAACAACAAATTTTTTGACGCAAAAAGTTGAC
TCTTTCTTTTTCGCATCTTTTATTGAGCAGGCGTGCAAAAAAAATAATAAGATGTCTCTC
GTCATACCTGAGAAGTTTCAACATATTTTGCGTATTATGAGTACCAATATCGATGGTAAA
CGCAAAGTTCCGGTCGCAATGACTGCCATCAAGGGTGTCGGTCGTCGTTACTCACACGTA
GTCCTCAGAAAAGCCGATGTTGATGTTGACAAACGTGCCGGTGAATGTACTGAGGAAGAA
GTGAGTCGAAAAAATTGTCACAATTATTTCCAATCCACGTCAATATAAAATTCCAGATTG
GTTTCTTAACAGACAAAAGGATATCATCGATGGTAAATATTCACAATTGACCTCTTCACT
CGTCGATTCAAAATTGCGTGAAGATTTGGAACGACTTAAGAAAATCCGTGCTCATCGTGG
TATGCGTCATTACTGGGGTCTTCGCGTTCGTGGTCAGCACACAAAAACAACCGGTCGTCG
CGGACGTACTGTTGGTGTGTCAAAGAAGAAGTAA
>g10508.t20 Gene=g10508 Length=135
MKLLKIKNYCLPENTSARQYGKNFFSKRCETTNFLTQKVDSFFFASFIEQACKKNNKMSL
VIPEKFQHILRIMSTNIDGKRKVPVAMTAIKGVGRRYSHVVLRKADVDVDKRAGECTEEE
VSRKNCHNYFQSTSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10508.t20 | Gene3D | G3DSA:1.10.8.50 | - | 58 | 128 | 0.00 |
| 2 | g10508.t20 | PANTHER | PTHR10871 | 30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18 | 54 | 121 | 0.00 |
| 3 | g10508.t20 | PANTHER | PTHR10871:SF3 | 40S RIBOSOMAL PROTEIN S18-RELATED | 54 | 121 | 0.00 |
| 1 | g10508.t20 | Pfam | PF00416 | Ribosomal protein S13/S18 | 71 | 123 | 0.00 |
| 6 | g10508.t20 | ProSiteProfiles | PS50159 | Ribosomal protein S13 family profile. | 72 | 123 | 15.11 |
| 4 | g10508.t20 | SUPERFAMILY | SSF46946 | S13-like H2TH domain | 70 | 122 | 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: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.
