General information for g13143.t1
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.t1 | TSS | g13143.t1 | 28151119 | 28151119 |
| chr_1 | g13143 | g13143.t1 | isoform | g13143.t1 | 28151137 | 28152591 |
| chr_1 | g13143 | g13143.t1 | exon | g13143.t1.exon1 | 28151137 | 28151139 |
| chr_1 | g13143 | g13143.t1 | cds | g13143.t1.CDS1 | 28151137 | 28151139 |
| chr_1 | g13143 | g13143.t1 | exon | g13143.t1.exon2 | 28151209 | 28151467 |
| chr_1 | g13143 | g13143.t1 | cds | g13143.t1.CDS2 | 28151209 | 28151467 |
| chr_1 | g13143 | g13143.t1 | exon | g13143.t1.exon3 | 28151695 | 28151792 |
| chr_1 | g13143 | g13143.t1 | cds | g13143.t1.CDS3 | 28151695 | 28151792 |
| chr_1 | g13143 | g13143.t1 | exon | g13143.t1.exon4 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t1 | cds | g13143.t1.CDS4 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t1 | TTS | g13143.t1 | 28152716 | 28152716 |
Sequences
>g13143.t1 Gene=g13143 Length=789
ATGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGCAGCTCCAAAAGCATGGATGCTG
GACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAACCGGTCCTCATAAATTGCGTGAA
TCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAAGTATGCTTTGACCAACACTGAA
ACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGATGGAAAAGTCAGAACAGATATC
AATTATCCAGCAGGTTTCATGGATGTCATCACCATTGAGAAAACTGGTGAATTCTTCCGT
TTGATCTATGATGTAAAGGGTCGTTTTACAATCCATCGCATTACTGCCGATGAAGCAAAA
TACAAGTTATGCAAAGTGAAGCGTGTAACAATTGGACCTAAGAAGATTCCATACTTGGTC
ACACATGATGGTCGTACACTCCGTTATCCAGATCCAAACATTCATGTAAACGACACAATT
CAATTAGATATTGCAACTGGAAAAATCACAGATCATATTCGTTTTGAATCCGGCAATTTG
GTTATGGTTACTGGAGGTCGTAACTTGGGTCGAGTTGGTACTGTTGTGAATCGTGAAAAG
CATCCTGGTTCATTTGAAATCATTCATGTGAAAGACGCTAATGGACATATGTTTGCTACT
CGTTTGACAAACATTTTCATCATCGGAAAAGGCGCAAAGGCATACATTTCATTGCCTAAA
GGCAAGGGTATTAAACTCAGTGTTGCCGAAGAACGCGATAAGCGATTGGCACAAAAAACC
ACTAACTAA
>g13143.t1 Gene=g13143 Length=262
MARGPKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTE
TKKIVMQRHIKVDGKVRTDINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAK
YKLCKVKRVTIGPKKIPYLVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFESGNL
VMVTGGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMFATRLTNIFIIGKGAKAYISLPK
GKGIKLSVAEERDKRLAQKTTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g13143.t1 | CDD | cd00165 | S4 | 44 | 112 | 2.40616E-6 |
| 14 | g13143.t1 | CDD | cd06087 | KOW_RPS4 | 175 | 229 | 1.60299E-28 |
| 10 | g13143.t1 | Gene3D | G3DSA:3.10.290.40 | - | 1 | 117 | 9.4E-61 |
| 12 | g13143.t1 | Gene3D | G3DSA:2.40.50.740 | - | 122 | 172 | 6.5E-29 |
| 11 | g13143.t1 | Gene3D | G3DSA:2.30.30.30 | - | 175 | 245 | 4.2E-36 |
| 8 | g13143.t1 | Hamap | MF_00485 | 30S ribosomal protein S4e [rps4e]. | 7 | 238 | 36.502556 |
| 6 | g13143.t1 | PANTHER | PTHR11581:SF30 | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | 1 | 259 | 2.7E-138 |
| 7 | g13143.t1 | PANTHER | PTHR11581 | 30S/40S RIBOSOMAL PROTEIN S4 | 1 | 259 | 2.7E-138 |
| 13 | g13143.t1 | PIRSF | PIRSF002116 | RPS4a_RPS4e | 1 | 241 | 8.6E-100 |
| 1 | g13143.t1 | Pfam | PF08071 | RS4NT (NUC023) domain | 3 | 39 | 8.1E-20 |
| 3 | g13143.t1 | Pfam | PF01479 | S4 domain | 43 | 90 | 1.4E-9 |
| 5 | g13143.t1 | Pfam | PF00900 | Ribosomal family S4e | 95 | 169 | 3.3E-36 |
| 2 | g13143.t1 | Pfam | PF00467 | KOW motif | 178 | 210 | 4.2E-6 |
| 4 | g13143.t1 | Pfam | PF16121 | 40S ribosomal protein S4 C-terminus | 212 | 259 | 6.3E-26 |
| 18 | g13143.t1 | ProSitePatterns | PS00528 | Ribosomal protein S4e signature. | 8 | 22 | - |
| 19 | g13143.t1 | ProSiteProfiles | PS50889 | S4 RNA-binding domain profile. | 42 | 105 | 10.755 |
| 16 | g13143.t1 | SMART | SM00363 | s4_6 | 42 | 106 | 2.2E-4 |
| 17 | g13143.t1 | SMART | SM00739 | kow_9 | 174 | 201 | 0.0023 |
| 9 | g13143.t1 | SUPERFAMILY | SSF55174 | Alpha-L RNA-binding motif | 51 | 134 | 2.36E-6 |
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 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