General information for g565.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S13.
Parent gene
- The parent gene g565 is located on chr_3: 4159867..4160610 (- 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_3 | g565 | g565.t23 | TTS | g565.t23 | 4159781 | 4159781 |
| chr_3 | g565 | g565.t23 | isoform | g565.t23 | 4159867 | 4160610 |
| chr_3 | g565 | g565.t23 | exon | g565.t23.exon1 | 4159867 | 4160165 |
| chr_3 | g565 | g565.t23 | cds | g565.t23.CDS1 | 4159867 | 4160165 |
| chr_3 | g565 | g565.t23 | exon | g565.t23.exon2 | 4160243 | 4160610 |
| chr_3 | g565 | g565.t23 | cds | g565.t23.CDS2 | 4160243 | 4160261 |
| chr_3 | g565 | g565.t23 | TSS | g565.t23 | 4160636 | 4160636 |
Sequences
>g565.t23 Gene=g565 Length=667
ATGGGTCGTATGCACGCGCCTGGGTAAGTTTTATATAGTTAATTCAAGCAAAAACTATTT
AAATATGTGATAAAAATGTGTACAAGTGTCGATTGTATAAAATAAATATGAAGTACAATA
GAGAAAAGTGTTATTTCATATGAAAAATAATGAAAATAATTTTTGCTTTTTAAGACAACA
AAAAACGTGTTCCGACATTTTTGATTCATACTAATGAATTTCTTTCTTTTCTCATTTTAG
TAAAGGTATTTCGCAATCTGCGTTACCTTATCGTCGATCAGTTCCATCATGGCTTAAACT
CAACGCTGAAGATGTCAAAGAACAAATCAAAAAGCTCGGAAAAAAGGGAATGACTCCATC
TCAAATTGTTCTCCGAGACAGTCATGGAGTCGCTCAGGTGCGTTTTGTTAATGGAAATAA
AATCCTCAGAATCATGAAAGCAGTCGGTTTGAAGCCAGACATTCCTGAAGACTTGTATTT
CCTCATCAAGCGTGCCGTCAGCATCCGTAAGCATTTAGAAAGAAATCGCAAGGATATTGA
CTCAAAATTCAGATTGATTTTGGTGGAATCAAGAATTCATCGCTTGGCTCGCTATTACAA
AAACAAAGCCGTTCTTCCACCAACATGGAAATATGAATCAGCAACTGCCTCAGCTTTAGT
TGCTTAA
>g565.t23 Gene=g565 Length=105
MTPSQIVLRDSHGVAQVRFVNGNKILRIMKAVGLKPDIPEDLYFLIKRAVSIRKHLERNR
KDIDSKFRLILVESRIHRLARYYKNKAVLPPTWKYESATASALVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g565.t23 | CDD | cd00353 | Ribosomal_S15p_S13e | 24 | 99 | 4.98021E-26 |
| 8 | g565.t23 | Gene3D | G3DSA:1.10.8.1030 | - | 1 | 36 | 2.0E-15 |
| 7 | g565.t23 | Gene3D | G3DSA:1.10.287.10 | - | 37 | 105 | 1.3E-37 |
| 2 | g565.t23 | PANTHER | PTHR11885:SF22 | 40S RIBOSOMAL PROTEIN S13 | 1 | 105 | 1.7E-50 |
| 3 | g565.t23 | PANTHER | PTHR11885 | RIBOSOMAL PROTEIN S15P/S13E | 1 | 105 | 1.7E-50 |
| 1 | g565.t23 | Pfam | PF00312 | Ribosomal protein S15 | 28 | 100 | 4.9E-16 |
| 6 | g565.t23 | ProSitePatterns | PS00362 | Ribosomal protein S15 signature. | 52 | 82 | - |
| 5 | g565.t23 | SMART | SM01387 | Ribosomal_S15_2 | 24 | 103 | 7.1E-15 |
| 4 | g565.t23 | SUPERFAMILY | SSF47060 | S15/NS1 RNA-binding domain | 20 | 96 | 2.38E-22 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g565/g565.t23; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g565.t23.fa.iupred3.txt does not exist
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. There were no conditions that were differentially expressed