General information for g11600.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 40S ribosomal protein S3.
Parent gene
- The parent gene g11600 is located on chr_1: 17409067..17410315 (- 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 | g11600 | g11600.t3 | TTS | g11600.t3 | 17408974 | 17408974 |
| chr_1 | g11600 | g11600.t3 | isoform | g11600.t3 | 17408976 | 17410315 |
| chr_1 | g11600 | g11600.t3 | exon | g11600.t3.exon1 | 17408976 | 17409574 |
| chr_1 | g11600 | g11600.t3 | cds | g11600.t3.CDS1 | 17409067 | 17409423 |
| chr_1 | g11600 | g11600.t3 | exon | g11600.t3.exon2 | 17409650 | 17409827 |
| chr_1 | g11600 | g11600.t3 | exon | g11600.t3.exon3 | 17410286 | 17410315 |
| chr_1 | g11600 | g11600.t3 | TSS | g11600.t3 | 17410361 | 17410361 |
Sequences
>g11600.t3 Gene=g11600 Length=807
ATGAACACTGCAATTTCAAAAAAACGCAAGTTTGTCGCCGCTGGCGTCTTTAAAGCTGAA
TTGAATGAGTTTTTAACTCGAGAGCTCGCAGAGGATGGATATTCAGGAGTTGAAGTACGT
GTGACACCATCAAGAACAGAAATCATTATTATGGCCACAAGAACTCAAAATGTTTTGGGT
GAAAAAGGTCGTCGTATTCGTGAATTAAATTCAATTTTGCACCCGGTGCAGTTGAATTGT
ATGCTGAAAAAGTTGCTACCCGTGGTCTCTGCGCTATTGCACAAGCCGAGTCTCTTCGAT
ACAAACTCATTGGTGGCTTAGCTGTTCGTCGTGCATGCTATGGTGTTCTTCGCTTCATTA
TGGAATCAGGAGCTAAGGGCTGCGAAGTTGTTGTATCTGGCAAACTTAGAGGTCAACGTG
CCAAGTCAATGAAATTTGTTGATGGGTTGATGATTCATTCAGGTGATCCTTGCAATGACT
ACGTTGATACAGCCACACGTCATGTCTTATTGAGACAAGGAGTATTGGGAATTAAGGTCA
AAATTATGCTACCATGGGATCCATCAGGCAAAATTGGTCCAAAACGACCATTGCCAGATA
ACGTTTCGGTTGTTGAACCTAAAGATGAGATCGTATATTTGAAACCTGACACCGAATACA
AAGGCAAACCAGCATATATTGGTGCTGAAGAACAGCAGCATGTCGAAGCTAAGTAAATAT
TTTCATATGAGTGCTGAAATATAAAACAACAATGGTGTTTTGTAAAACGTTAAGATCATA
ATCAATAAAAAACACATTTGAATTCCA
>g11600.t3 Gene=g11600 Length=118
MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTATRHVLLRQGVLGIKV
KIMLPWDPSGKIGPKRPLPDNVSVVEPKDEIVYLKPDTEYKGKPAYIGAEEQQHVEAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11600.t3 | Gene3D | G3DSA:3.30.1140.32 | - | 1 | 95 | 3.4E-51 |
| 2 | g11600.t3 | PANTHER | PTHR11760:SF36 | 40S RIBOSOMAL PROTEIN S3 | 1 | 107 | 1.2E-55 |
| 3 | g11600.t3 | PANTHER | PTHR11760 | 30S/40S RIBOSOMAL PROTEIN S3 | 1 | 107 | 1.2E-55 |
| 1 | g11600.t3 | Pfam | PF00189 | Ribosomal protein S3, C-terminal domain | 1 | 62 | 2.8E-17 |
| 5 | g11600.t3 | ProSitePatterns | PS00548 | Ribosomal protein S3 signature. | 21 | 57 | - |
| 4 | g11600.t3 | SUPERFAMILY | SSF54821 | Ribosomal protein S3 C-terminal domain | 1 | 65 | 1.07E-19 |
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: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.
