General information for g13143.t80
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.t80 | TSS | g13143.t80 | 28150713 | 28150713 |
| chr_1 | g13143 | g13143.t80 | isoform | g13143.t80 | 28150731 | 28152591 |
| chr_1 | g13143 | g13143.t80 | exon | g13143.t80.exon1 | 28150731 | 28150739 |
| chr_1 | g13143 | g13143.t80 | exon | g13143.t80.exon2 | 28151190 | 28151467 |
| chr_1 | g13143 | g13143.t80 | cds | g13143.t80.CDS1 | 28151423 | 28151467 |
| chr_1 | g13143 | g13143.t80 | exon | g13143.t80.exon3 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t80 | cds | g13143.t80.CDS2 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t80 | TTS | g13143.t80 | 28152716 | 28152716 |
Sequences
>g13143.t80 Gene=g13143 Length=716
CCTAAGTAATTATTTCTTGTGATTGTAGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTT
AGCAGCTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATC
AACCGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTT
GAAGTATGCTTTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCAAAGT
TGATGGAAAAGTCAGAACAGATATCAATTATCCAGCAGGTTTCATGGTACAAGTTATGCA
AAGTGAAGCGTGTAACAATTGGACCTAAGAAGATTCCATACTTGGTCACACATGATGGTC
GTACACTCCGTTATCCAGATCCAAACATTCATGTAAACGACACAATTCAATTAGATATTG
CAACTGGAAAAATCACAGATCATATTCGTTTTGAATCCGGCAATTTGGTTATGGTTACTG
GAGGTCGTAACTTGGGTCGAGTTGGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCAT
TTGAAATCATTCATGTGAAAGACGCTAATGGACATATGTTTGCTACTCGTTTGACAAACA
TTTTCATCATCGGAAAAGGCGCAAAGGCATACATTTCATTGCCTAAAGGCAAGGGTATTA
AACTCAGTGTTGCCGAAGAACGCGATAAGCGATTGGCACAAAAAACCACTAACTAA
>g13143.t80 Gene=g13143 Length=157
MEKSEQISIIQQVSWYKLCKVKRVTIGPKKIPYLVTHDGRTLRYPDPNIHVNDTIQLDIA
TGKITDHIRFESGNLVMVTGGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMFATRLTNI
FIIGKGAKAYISLPKGKGIKLSVAEERDKRLAQKTTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13143.t80 | CDD | cd06087 | KOW_RPS4 | 70 | 124 | 0.0e+00 |
| 7 | g13143.t80 | Gene3D | G3DSA:2.40.50.740 | - | 17 | 67 | 0.0e+00 |
| 6 | g13143.t80 | Gene3D | G3DSA:2.30.30.30 | - | 70 | 140 | 0.0e+00 |
| 4 | g13143.t80 | PANTHER | PTHR11581 | 30S/40S RIBOSOMAL PROTEIN S4 | 9 | 152 | 0.0e+00 |
| 3 | g13143.t80 | Pfam | PF00900 | Ribosomal family S4e | 13 | 64 | 0.0e+00 |
| 1 | g13143.t80 | Pfam | PF00467 | KOW motif | 73 | 105 | 1.9e-06 |
| 2 | g13143.t80 | Pfam | PF16121 | 40S ribosomal protein S4 C-terminus | 107 | 154 | 0.0e+00 |
| 5 | g13143.t80 | SMART | SM00739 | kow_9 | 69 | 96 | 2.3e-03 |
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 transcript has been annotated with K02987 (small subunit ribosomal protein S4e)
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. There were no conditions that were differentially expressed