General information for g13143.t40
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.t40 | TSS | g13143.t40 | 28150713 | 28150713 |
| chr_1 | g13143 | g13143.t40 | isoform | g13143.t40 | 28150723 | 28152591 |
| chr_1 | g13143 | g13143.t40 | exon | g13143.t40.exon1 | 28150723 | 28150739 |
| chr_1 | g13143 | g13143.t40 | exon | g13143.t40.exon2 | 28151209 | 28151471 |
| chr_1 | g13143 | g13143.t40 | cds | g13143.t40.CDS1 | 28151423 | 28151471 |
| chr_1 | g13143 | g13143.t40 | exon | g13143.t40.exon3 | 28151695 | 28151792 |
| chr_1 | g13143 | g13143.t40 | cds | g13143.t40.CDS2 | 28151695 | 28151792 |
| chr_1 | g13143 | g13143.t40 | exon | g13143.t40.exon4 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t40 | cds | g13143.t40.CDS3 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t40 | TTS | g13143.t40 | 28152716 | 28152716 |
Sequences
>g13143.t40 Gene=g13143 Length=807
TTGTCAATCCTAAGTAAGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGCAGCTCCAA
AAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAACCGGTCCTC
ATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAAGTATGCTT
TGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGATGGAAAAG
TCAGAACAGATATCAATTATCCAGCAGGTTTCATGGGTAAATGTCATCACCATTGAGAAA
ACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACAATCCATCGCATT
ACTGCCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGCGTGTAACAATTGGACCTAAG
AAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCCAGATCCAAACATT
CATGTAAACGACACAATTCAATTAGATATTGCAACTGGAAAAATCACAGATCATATTCGT
TTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGGTCGAGTTGGTACT
GTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTGAAAGACGCTAAT
GGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAAGGCGCAAAGGCA
TACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAAGAACGCGATAAG
CGATTGGCACAAAAAACCACTAACTAA
>g13143.t40 Gene=g13143 Length=191
MEKSEQISIIQQVSWVNVITIEKTGEFFRLIYDVKGRFTIHRITADEAKYKLCKVKRVTI
GPKKIPYLVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFESGNLVMVTGGRNLGR
VGTVVNREKHPGSFEIIHVKDANGHMFATRLTNIFIIGKGAKAYISLPKGKGIKLSVAEE
RDKRLAQKTTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g13143.t40 | CDD | cd06087 | KOW_RPS4 | 104 | 158 | 0.0e+00 |
| 6 | g13143.t40 | Gene3D | G3DSA:3.10.290.40 | - | 7 | 46 | 0.0e+00 |
| 8 | g13143.t40 | Gene3D | G3DSA:2.40.50.740 | - | 51 | 101 | 0.0e+00 |
| 7 | g13143.t40 | Gene3D | G3DSA:2.30.30.30 | - | 104 | 174 | 0.0e+00 |
| 4 | g13143.t40 | PANTHER | PTHR11581 | 30S/40S RIBOSOMAL PROTEIN S4 | 14 | 186 | 0.0e+00 |
| 3 | g13143.t40 | Pfam | PF00900 | Ribosomal family S4e | 24 | 98 | 0.0e+00 |
| 1 | g13143.t40 | Pfam | PF00467 | KOW motif | 107 | 139 | 2.6e-06 |
| 2 | g13143.t40 | Pfam | PF16121 | 40S ribosomal protein S4 C-terminus | 141 | 188 | 0.0e+00 |
| 5 | g13143.t40 | SMART | SM00739 | kow_9 | 103 | 130 | 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 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