General information for g11474.t18
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 40S ribosomal protein S6.
Parent gene
- The parent gene g11474 is located on chr_1: 16438523..16438986 (- 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 | g11474 | g11474.t18 | TTS | g11474.t18 | 16437300 | 16437300 |
| chr_1 | g11474 | g11474.t18 | isoform | g11474.t18 | 16437372 | 16438269 |
| chr_1 | g11474 | g11474.t18 | exon | g11474.t18.exon1 | 16437372 | 16437855 |
| chr_1 | g11474 | g11474.t18 | cds | g11474.t18.CDS1 | 16437838 | 16437855 |
| chr_1 | g11474 | g11474.t18 | exon | g11474.t18.exon2 | 16437937 | 16438269 |
| chr_1 | g11474 | g11474.t18 | cds | g11474.t18.CDS2 | 16437937 | 16438269 |
| chr_1 | g11474 | g11474.t18 | TSS | g11474.t18 | 16438988 | 16438988 |
Sequences
>g11474.t18 Gene=g11474 Length=817
CTTAAAAAAGGACATTCCTGTTATCGTCCAAGAAGAACTGGAGAACGTAAACGTAAATCA
GTTCGTGGTTGCATTGTTGATCAAAACTTGTCAGCTCTCGCTTTGATCGTCGTACGTAAG
GGTGAGAGTGAAGTTGAAGGTTTAACTGATGTCACCGTTCCTCGTCGTCTCGGACCTAAA
CGTGCAAGCCACATTCGTAAACTGTTTGCTTTGACAAAAGAGGATGATGTTCGCAAGTAT
GTCATTAAGAAGCCTTTGCCACCAAAAGAGGGCAAAAAGCAACGTTTTCAAGCTCCTAGA
ATTCAACGTTTAGTAACACCGGTCGTTTTACAGACATCGTTTGGCTCTTAAAAAACGCCG
AGTTGAATCACGCAAAGAAGCTGAAGCTGAATATGCAAAATTATTAGCTCAGCGTAGACG
TGAAGAAAAACTTCGTCGTCGTACACGTTCAGCATCTATTCGTGAATCAAAGAGCTCAAT
TTCATCAGATAAAGATAGCAAGAAAGAAGTTAAGAAGCCAGAAGTTGTCAAGAAAGTTGA
AGCTAAACCAGCAAAGAAGGTTGAAGAGAAGAAAAAGGTTGATGACAAAAAGAAACCAGC
TGAAAAGAAAGTTGAAACTAAAAAGGGTGATGCAAAAGCCGCCGCTGTAAAGAAGATTGA
AGAAAAGAAAAAGCCAGCCCAAGCTGAGAAGAAATCTGCAGACAAAAAACCAGCAGCTGC
ACCAGCAAAGAAAGAGGCCCCAAAGCCTGCAACAGCACCATCAGCCAAGAAGGAAGCATC
TAAACCAACAGATGCAAAGAAGCCCAAAAAAAAGTAA
>g11474.t18 Gene=g11474 Length=116
LKKGHSCYRPRRTGERKRKSVRGCIVDQNLSALALIVVRKGESEVEGLTDVTVPRRLGPK
RASHIRKLFALTKEDDVRKYVIKKPLPPKEGKKQRFQAPRIQRLVTPVVLQTSFGS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g11474.t18 | PANTHER | PTHR11502:SF6 | 40S RIBOSOMAL PROTEIN S6 | 1 | 112 | 0.0e+00 |
| 3 | g11474.t18 | PANTHER | PTHR11502 | 40S RIBOSOMAL PROTEIN S6 | 1 | 112 | 0.0e+00 |
| 1 | g11474.t18 | Pfam | PF01092 | Ribosomal protein S6e | 1 | 50 | 0.0e+00 |
| 4 | g11474.t18 | SMART | SM01405 | Ribosomal_S6e_2 | 1 | 50 | 8.2e-05 |
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 |
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.
