General information for g565.t1
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.t1 | TTS | g565.t1 | 4159781 | 4159781 |
| chr_3 | g565 | g565.t1 | isoform | g565.t1 | 4159867 | 4160610 |
| chr_3 | g565 | g565.t1 | exon | g565.t1.exon1 | 4159867 | 4160171 |
| chr_3 | g565 | g565.t1 | cds | g565.t1.CDS1 | 4159867 | 4160171 |
| chr_3 | g565 | g565.t1 | exon | g565.t1.exon2 | 4160243 | 4160370 |
| chr_3 | g565 | g565.t1 | cds | g565.t1.CDS2 | 4160243 | 4160370 |
| chr_3 | g565 | g565.t1 | exon | g565.t1.exon3 | 4160588 | 4160610 |
| chr_3 | g565 | g565.t1 | cds | g565.t1.CDS3 | 4160588 | 4160610 |
| chr_3 | g565 | g565.t1 | TSS | g565.t1 | 4160636 | 4160636 |
Sequences
>g565.t1 Gene=g565 Length=456
ATGGGTCGTATGCACGCGCCTGGTAAAGGTATTTCGCAATCTGCGTTACCTTATCGTCGA
TCAGTTCCATCATGGCTTAAACTCAACGCTGAAGATGTCAAAGAACAAATCAAAAAGCTC
GGAAAAAAGGGAATGACTCCATCTCAAATTGGTATTATTCTCCGAGACAGTCATGGAGTC
GCTCAGGTGCGTTTTGTTAATGGAAATAAAATCCTCAGAATCATGAAAGCAGTCGGTTTG
AAGCCAGACATTCCTGAAGACTTGTATTTCCTCATCAAGCGTGCCGTCAGCATCCGTAAG
CATTTAGAAAGAAATCGCAAGGATATTGACTCAAAATTCAGATTGATTTTGGTGGAATCA
AGAATTCATCGCTTGGCTCGCTATTACAAAAACAAAGCCGTTCTTCCACCAACATGGAAA
TATGAATCAGCAACTGCCTCAGCTTTAGTTGCTTAA
>g565.t1 Gene=g565 Length=151
MGRMHAPGKGISQSALPYRRSVPSWLKLNAEDVKEQIKKLGKKGMTPSQIGIILRDSHGV
AQVRFVNGNKILRIMKAVGLKPDIPEDLYFLIKRAVSIRKHLERNRKDIDSKFRLILVES
RIHRLARYYKNKAVLPPTWKYESATASALVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g565.t1 | CDD | cd00353 | Ribosomal_S15p_S13e | 70 | 145 | 1.33752E-25 |
| 7 | g565.t1 | Gene3D | G3DSA:1.10.8.1030 | - | 35 | 82 | 9.0E-26 |
| 6 | g565.t1 | Gene3D | G3DSA:1.10.287.10 | - | 83 | 151 | 3.6E-37 |
| 4 | g565.t1 | Hamap | MF_01343_A | 30S ribosomal protein S15 [rpsO]. | 3 | 149 | 31.278294 |
| 3 | g565.t1 | PANTHER | PTHR11885 | RIBOSOMAL PROTEIN S15P/S13E | 1 | 151 | 1.3E-77 |
| 2 | g565.t1 | Pfam | PF08069 | Ribosomal S13/S15 N-terminal domain | 1 | 60 | 4.4E-30 |
| 1 | g565.t1 | Pfam | PF00312 | Ribosomal protein S15 | 74 | 146 | 1.4E-15 |
| 9 | g565.t1 | ProSitePatterns | PS00362 | Ribosomal protein S15 signature. | 98 | 128 | - |
| 10 | g565.t1 | SMART | SM01386 | Ribosomal_S13_N_2 | 1 | 60 | 6.0E-38 |
| 11 | g565.t1 | SMART | SM01387 | Ribosomal_S15_2 | 70 | 149 | 7.1E-15 |
| 5 | g565.t1 | SUPERFAMILY | SSF47060 | S15/NS1 RNA-binding domain | 66 | 142 | 7.06E-22 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g565/g565.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g565.t1.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 transcript has been annotated with K02953 (small subunit ribosomal protein S13e)
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.
