General information for g11431.t25
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 40S ribosomal protein S15.
Parent gene
- The parent gene g11431 is located on chr_1: 16196226..16199772 (+ 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 | g11431 | g11431.t25 | TSS | g11431.t25 | 16195537 | 16195537 |
| chr_1 | g11431 | g11431.t25 | isoform | g11431.t25 | 16195568 | 16196344 |
| chr_1 | g11431 | g11431.t25 | exon | g11431.t25.exon1 | 16195568 | 16195576 |
| chr_1 | g11431 | g11431.t25 | cds | g11431.t25.CDS1 | 16195568 | 16195576 |
| chr_1 | g11431 | g11431.t25 | exon | g11431.t25.exon2 | 16195640 | 16195951 |
| chr_1 | g11431 | g11431.t25 | cds | g11431.t25.CDS2 | 16195640 | 16195951 |
| chr_1 | g11431 | g11431.t25 | exon | g11431.t25.exon3 | 16196231 | 16196344 |
| chr_1 | g11431 | g11431.t25 | cds | g11431.t25.CDS3 | 16196231 | 16196344 |
| chr_1 | g11431 | g11431.t25 | TTS | g11431.t25 | 16196443 | 16196443 |
Sequences
>g11431.t25 Gene=g11431 Length=435
ATGGCTGATGCTCAAGAAGAACAAGTTCGCAAGAAGCGTACCTTCCGTAAATTTACATAT
CGTGGAGTTGATTTAGATCAACTTTTGGATATGCCAAATGAACAACTCTCAGAGTTGATG
CATAGTCGTGCTCGTCGTCGTTTTGCTCGTGGATTGAAACGCAAACCAATGGCTTTAATC
CAAAAGTTGCGAAAGGCAAAGAAAGAGGCACCTCCACTTGAGAAGCCAGCTATTGTTAAG
ACTCATTTGCGTGACATGATCATTGTACCCGAAATGGTTGGATCAATCGTCGGTATCTAT
AATGGAAAAACATTCAATCAACCAGAAATGATTGGACACTATTTAGGAGACTTTTCGCTC
ACATATAAACCAGTTAAGCATGGTCGTCCCGGTATTGGTGCCACGCACAGTTCACGATTT
ATTCCATTAAAGTAA
>g11431.t25 Gene=g11431 Length=144
MADAQEEQVRKKRTFRKFTYRGVDLDQLLDMPNEQLSELMHSRARRRFARGLKRKPMALI
QKLRKAKKEAPPLEKPAIVKTHLRDMIIVPEMVGSIVGIYNGKTFNQPEMIGHYLGDFSL
TYKPVKHGRPGIGATHSSRFIPLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11431.t25 | Gene3D | G3DSA:3.30.860.20 | - | 4 | 144 | 0.00000 |
| 4 | g11431.t25 | Hamap | MF_00531 | 30S ribosomal protein S19 [rpsS]. | 44 | 133 | 18.12008 |
| 2 | g11431.t25 | PANTHER | PTHR11880 | RIBOSOMAL PROTEIN S19P FAMILY MEMBER | 3 | 144 | 0.00000 |
| 3 | g11431.t25 | PANTHER | PTHR11880:SF2 | 40S RIBOSOMAL PROTEIN S15 | 3 | 144 | 0.00000 |
| 8 | g11431.t25 | PIRSF | PIRSF002144 | RPS19p_RPS19a_RPS15e_RPS19o | 1 | 144 | 0.00000 |
| 1 | g11431.t25 | Pfam | PF00203 | Ribosomal protein S19 | 46 | 127 | 0.00000 |
| 5 | g11431.t25 | SUPERFAMILY | SSF54570 | Ribosomal protein S19 | 52 | 128 | 0.00000 |
| 7 | g11431.t25 | TIGRFAM | TIGR01025 | uS19_arch: ribosomal protein uS19 | 15 | 144 | 0.00000 |
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:0015935 | small ribosomal subunit | CC |
KEGG
Orthology
- This transcript has been annotated with K02958 (small subunit ribosomal protein S15e)
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.
