General information for g13143.t47
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.t47 | TSS | g13143.t47 | 28150713 | 28150713 |
| chr_1 | g13143 | g13143.t47 | isoform | g13143.t47 | 28150723 | 28152591 |
| chr_1 | g13143 | g13143.t47 | exon | g13143.t47.exon1 | 28150723 | 28150739 |
| chr_1 | g13143 | g13143.t47 | exon | g13143.t47.exon2 | 28151194 | 28151467 |
| chr_1 | g13143 | g13143.t47 | cds | g13143.t47.CDS1 | 28151260 | 28151467 |
| chr_1 | g13143 | g13143.t47 | exon | g13143.t47.exon3 | 28151695 | 28151792 |
| chr_1 | g13143 | g13143.t47 | cds | g13143.t47.CDS2 | 28151695 | 28151792 |
| chr_1 | g13143 | g13143.t47 | exon | g13143.t47.exon4 | 28152163 | 28152253 |
| chr_1 | g13143 | g13143.t47 | cds | g13143.t47.CDS3 | 28152163 | 28152253 |
| chr_1 | g13143 | g13143.t47 | exon | g13143.t47.exon5 | 28152314 | 28152591 |
| chr_1 | g13143 | g13143.t47 | cds | g13143.t47.CDS4 | 28152314 | 28152591 |
| chr_1 | g13143 | g13143.t47 | TTS | g13143.t47 | 28152716 | 28152716 |
Sequences
>g13143.t47 Gene=g13143 Length=758
TTGTCAATCCTAAGTAATTCTTGTGATTGTAGGCTCGCGGTCCGAAAAAACATTTGAAGC
GTTTAGCAGCTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTC
CATCAACCGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATC
GCTTGAAGTATGCTTTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCA
AAGTTGATGGAAAAGTCAGAACAGATATCAATTATCCAGCAGGTTTCATGGATGTCATCA
CCATTGAGAAAACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACAA
TCCATCGCATTACTGCCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGCGTGTAACAA
TTGGACCTAAGAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCCAG
ATCATATTCGTTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGGTC
GAGTTGGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTGA
AAGACGCTAATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAAG
GCGCAAAGGCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAAG
AACGCGATAAGCGATTGGCACAAAAAACCACTAACTAA
>g13143.t47 Gene=g13143 Length=224
MLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTETKKIVMQRHIKVDGKVRT
DINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAKYKLCKVKRVTIGPKKIPY
LVTHDGRTLRYPDHIRFESGNLVMVTGGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMF
ATRLTNIFIIGKGAKAYISLPKGKGIKLSVAEERDKRLAQKTTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g13143.t47 | CDD | cd00165 | S4 | 26 | 94 | 0.0000024 |
| 16 | g13143.t47 | CDD | cd06087 | KOW_RPS4 | 137 | 191 | 0.0000000 |
| 11 | g13143.t47 | Gene3D | G3DSA:3.10.290.40 | - | 1 | 99 | 0.0000000 |
| 13 | g13143.t47 | Gene3D | G3DSA:2.40.50.740 | - | 104 | 137 | 0.0000000 |
| 12 | g13143.t47 | Gene3D | G3DSA:2.30.30.30 | - | 138 | 207 | 0.0000000 |
| 6 | g13143.t47 | PANTHER | PTHR11581:SF30 | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | 1 | 134 | 0.0000000 |
| 8 | g13143.t47 | PANTHER | PTHR11581 | 30S/40S RIBOSOMAL PROTEIN S4 | 1 | 134 | 0.0000000 |
| 7 | g13143.t47 | PANTHER | PTHR11581:SF30 | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | 133 | 221 | 0.0000000 |
| 9 | g13143.t47 | PANTHER | PTHR11581 | 30S/40S RIBOSOMAL PROTEIN S4 | 133 | 221 | 0.0000000 |
| 14 | g13143.t47 | PIRSF | PIRSF002116 | RPS4a_RPS4e | 1 | 134 | 0.0000000 |
| 15 | g13143.t47 | PIRSF | PIRSF002116 | RPS4a_RPS4e | 132 | 203 | 0.0000000 |
| 1 | g13143.t47 | Pfam | PF08071 | RS4NT (NUC023) domain | 1 | 21 | 0.0000001 |
| 3 | g13143.t47 | Pfam | PF01479 | S4 domain | 25 | 72 | 0.0000000 |
| 5 | g13143.t47 | Pfam | PF00900 | Ribosomal family S4e | 77 | 135 | 0.0000000 |
| 2 | g13143.t47 | Pfam | PF00467 | KOW motif | 140 | 172 | 0.0000033 |
| 4 | g13143.t47 | Pfam | PF16121 | 40S ribosomal protein S4 C-terminus | 174 | 221 | 0.0000000 |
| 20 | g13143.t47 | ProSiteProfiles | PS50889 | S4 RNA-binding domain profile. | 24 | 87 | 10.7550000 |
| 18 | g13143.t47 | SMART | SM00363 | s4_6 | 24 | 88 | 0.0002200 |
| 19 | g13143.t47 | SMART | SM00739 | kow_9 | 136 | 163 | 0.0023000 |
| 10 | g13143.t47 | SUPERFAMILY | SSF55174 | Alpha-L RNA-binding motif | 33 | 116 | 0.0000013 |
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:0003723 | RNA binding | MF |
| 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