General information for g13143.t92
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S4.
Parent gene
- The parent gene g13143 is located on chr_1: 28152163..28161163 (+ 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 | g13143 | g13143.t92 | TSS | g13143.t92 | 28151119 | 28151119 |
| chr_1 | g13143 | g13143.t92 | isoform | g13143.t92 | 28151137 | 28152591 |
| chr_1 | g13143 | g13143.t92 | exon | g13143.t92.exon1 | 28151137 | 28151139 |
| chr_1 | g13143 | g13143.t92 | cds | g13143.t92.CDS1 | 28151137 | 28151139 |
| chr_1 | g13143 | g13143.t92 | exon | g13143.t92.exon2 | 28151209 | 28151422 |
| chr_1 | g13143 | g13143.t92 | cds | g13143.t92.CDS2 | 28151209 | 28151422 |
| chr_1 | g13143 | g13143.t92 | exon | g13143.t92.exon3 | 28151740 | 28151792 |
| chr_1 | g13143 | g13143.t92 | cds | g13143.t92.CDS3 | 28151740 | 28151792 |
| chr_1 | g13143 | g13143.t92 | exon | g13143.t92.exon4 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t92 | cds | g13143.t92.CDS4 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t92 | TTS | g13143.t92 | 28152716 | 28152716 |
Sequences
>g13143.t92 Gene=g13143 Length=699
ATGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGCAGCTCCAAAAGCATGGATGCTG
GACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAACCGGTCCTCATAAATTGCGTGAA
TCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAAGTATGCTTTGACCAACACTGAA
ACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGATGATGTAAAGGGTCGTTTTACA
ATCCATCGCATTACTGCCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGCGTGTAACA
ATTGGACCTAAGAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCCA
GATCCAAACATTCATGTAAACGACACAATTCAATTAGATATTGCAACTGGAAAAATCACA
GATCATATTCGTTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGGT
CGAGTTGGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTG
AAAGACGCTAATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAA
GGCGCAAAGGCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAA
GAACGCGATAAGCGATTGGCACAAAAAACCACTAACTAA
>g13143.t92 Gene=g13143 Length=232
MARGPKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTE
TKKIVMQRHIKVDDVKGRFTIHRITADEAKYKLCKVKRVTIGPKKIPYLVTHDGRTLRYP
DPNIHVNDTIQLDIATGKITDHIRFESGNLVMVTGGRNLGRVGTVVNREKHPGSFEIIHV
KDANGHMFATRLTNIFIIGKGAKAYISLPKGKGIKLSVAEERDKRLAQKTTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g13143.t92 | CDD | cd06087 | KOW_RPS4 | 145 | 199 | 2.56111E-29 |
| 11 | g13143.t92 | Gene3D | G3DSA:3.10.290.40 | - | 1 | 76 | 9.2E-35 |
| 13 | g13143.t92 | Gene3D | G3DSA:2.40.50.740 | - | 92 | 142 | 5.3E-29 |
| 12 | g13143.t92 | Gene3D | G3DSA:2.30.30.30 | - | 145 | 215 | 3.4E-36 |
| 6 | g13143.t92 | PANTHER | PTHR11581:SF30 | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | 1 | 73 | 1.5E-111 |
| 8 | g13143.t92 | PANTHER | PTHR11581 | 30S/40S RIBOSOMAL PROTEIN S4 | 1 | 73 | 1.5E-111 |
| 5 | g13143.t92 | PANTHER | PTHR11581:SF30 | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | 73 | 229 | 1.5E-111 |
| 7 | g13143.t92 | PANTHER | PTHR11581 | 30S/40S RIBOSOMAL PROTEIN S4 | 73 | 229 | 1.5E-111 |
| 15 | g13143.t92 | PIRSF | PIRSF002116 | RPS4a_RPS4e | 1 | 78 | 1.6E-30 |
| 14 | g13143.t92 | PIRSF | PIRSF002116 | RPS4a_RPS4e | 73 | 211 | 1.5E-45 |
| 1 | g13143.t92 | Pfam | PF08071 | RS4NT (NUC023) domain | 3 | 39 | 6.7E-20 |
| 4 | g13143.t92 | Pfam | PF00900 | Ribosomal family S4e | 74 | 139 | 1.2E-30 |
| 2 | g13143.t92 | Pfam | PF00467 | KOW motif | 148 | 180 | 3.5E-6 |
| 3 | g13143.t92 | Pfam | PF16121 | 40S ribosomal protein S4 C-terminus | 182 | 229 | 5.2E-26 |
| 10 | g13143.t92 | ProSitePatterns | PS00528 | Ribosomal protein S4e signature. | 8 | 22 | - |
| 9 | g13143.t92 | SMART | SM00739 | kow_9 | 144 | 171 | 0.0023 |
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. There were no conditions that were differentially expressed