General information for g10408.t42
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S3a.
Parent gene
- The parent gene g10408 is located on chr_1: 9593039..9594359 (+ 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 | g10408 | g10408.t42 | isoform | g10408.t42 | 9592031 | 9593133 |
| chr_1 | g10408 | g10408.t42 | exon | g10408.t42.exon1 | 9592031 | 9592052 |
| chr_1 | g10408 | g10408.t42 | cds | g10408.t42.CDS1 | 9592031 | 9592052 |
| chr_1 | g10408 | g10408.t42 | exon | g10408.t42.exon2 | 9592186 | 9592504 |
| chr_1 | g10408 | g10408.t42 | cds | g10408.t42.CDS2 | 9592186 | 9592504 |
| chr_1 | g10408 | g10408.t42 | exon | g10408.t42.exon3 | 9592605 | 9592914 |
| chr_1 | g10408 | g10408.t42 | cds | g10408.t42.CDS3 | 9592605 | 9592914 |
| chr_1 | g10408 | g10408.t42 | exon | g10408.t42.exon4 | 9593069 | 9593133 |
| chr_1 | g10408 | g10408.t42 | cds | g10408.t42.CDS4 | 9593069 | 9593131 |
| chr_1 | g10408 | g10408.t42 | TTS | g10408.t42 | 9593229 | 9593229 |
| chr_1 | g10408 | g10408.t42 | TSS | g10408.t42 | NA | NA |
Sequences
>g10408.t42 Gene=g10408 Length=716
ATGGCAGTCGGAAAAAATAAAGGTTTAGCCAAAGGTGGCAAGAAAGGAACCAAGAAGAAG
ATTGTGGATCCCTTCACACGTAAGGACTGGTATGATATCAAAGCTCCATCAATGTTCACC
ACACGCCAAGTGGGAAAGACATTGGTCAATCGTACACAAGGTACAAAAATTGCTAGCGAA
GGCTTGAAAGGTCGCGTGTTTGAAGTCTCATTAGCTGATTTACAAAACGACAATGATGCC
GAGAGATCTTTCCGCAAATTCAAGCTTATCGCTGAAGACGTTCAAGGACGAAATGTCCTC
ACAAATTTCCATGGAATGGACTTAACAACTGATAAATTGAGATCGATGGTGAAGAAATGG
CAAACATTGATTGAATGTCATGTTGATGTCAAAACAACCGATGGTTACGTTTTGCGTGTA
TTCTGCATTGGATTTACTGCAAAAGATAGTTCATCGCATCGCAAAACTTGTTACGCTCAA
ACCTCTCAAATCAAAACAATTCGCAAAAAGATGACTGACATCATCACACGCGACATTTCA
AGCTCTGACTTGAAGGAAGTTGTCAACAAATTGTTGCCAGACTCAATTGCAAAGGATATT
GAGAAGGCCTGTCATGGAGTCTATCCTCTTCATGATGTGTACATTCGCAAGCTGCAGAAG
GAGTTGCCGTTGAAAGACCAGAAGGATATGAACCACCAGTCCAAGCCGCAGTTTAA
>g10408.t42 Gene=g10408 Length=238
MAVGKNKGLAKGGKKGTKKKIVDPFTRKDWYDIKAPSMFTTRQVGKTLVNRTQGTKIASE
GLKGRVFEVSLADLQNDNDAERSFRKFKLIAEDVQGRNVLTNFHGMDLTTDKLRSMVKKW
QTLIECHVDVKTTDGYVLRVFCIGFTAKDSSSHRKTCYAQTSQIKTIRKKMTDIITRDIS
SSDLKEVVNKLLPDSIAKDIEKACHGVYPLHDVYIRKLQKELPLKDQKDMNHQSKPQF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10408.t42 | Hamap | MF_03122 | 40S ribosomal protein S1 [RPS3A]. | 1 | 238 | 35.468899 |
| 2 | g10408.t42 | PANTHER | PTHR11830 | 40S RIBOSOMAL PROTEIN S3A | 1 | 219 | 2.3E-101 |
| 3 | g10408.t42 | PANTHER | PTHR11830:SF34 | 40S RIBOSOMAL PROTEIN S3A | 1 | 219 | 2.3E-101 |
| 1 | g10408.t42 | Pfam | PF01015 | Ribosomal S3Ae family | 17 | 218 | 4.1E-83 |
| 6 | g10408.t42 | ProSitePatterns | PS01191 | Ribosomal protein S3Ae signature. | 62 | 74 | - |
| 5 | g10408.t42 | SMART | SM01397 | Ribosomal_S3Ae_2 | 16 | 221 | 1.6E-130 |
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.
