General information for g13143.t2
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.t2 | isoform | g13143.t2 | 28149610 | 28152591 |
| chr_1 | g13143 | g13143.t2 | exon | g13143.t2.exon1 | 28149610 | 28149686 |
| chr_1 | g13143 | g13143.t2 | cds | g13143.t2.CDS1 | 28149675 | 28149686 |
| chr_1 | g13143 | g13143.t2 | exon | g13143.t2.exon2 | 28151209 | 28151467 |
| chr_1 | g13143 | g13143.t2 | cds | g13143.t2.CDS2 | 28151209 | 28151467 |
| chr_1 | g13143 | g13143.t2 | exon | g13143.t2.exon3 | 28151695 | 28151792 |
| chr_1 | g13143 | g13143.t2 | cds | g13143.t2.CDS3 | 28151695 | 28151792 |
| chr_1 | g13143 | g13143.t2 | exon | g13143.t2.exon4 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t2 | cds | g13143.t2.CDS4 | 28152163 | 28152591 |
| chr_1 | g13143 | g13143.t2 | TTS | g13143.t2 | 28152716 | 28152716 |
| chr_1 | g13143 | g13143.t2 | TSS | g13143.t2 | NA | NA |
Sequences
>g13143.t2 Gene=g13143 Length=863
CTACTCAGCTATATGAATATTTTCTGATGATACAATAATTGTTTTTGCATTGAAATCTTT
TTGAAATGAAACATAAGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGCAGCTCCAA
AAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAACCGGTCCTC
ATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAAGTATGCTT
TGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGATGGAAAAG
TCAGAACAGATATCAATTATCCAGCAGGTTTCATGGATGTCATCACCATTGAGAAAACTG
GTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACAATCCATCGCATTACTG
CCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGCGTGTAACAATTGGACCTAAGAAGA
TTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCCAGATCCAAACATTCATG
TAAACGACACAATTCAATTAGATATTGCAACTGGAAAAATCACAGATCATATTCGTTTTG
AATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGGTCGAGTTGGTACTGTTG
TGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTGAAAGACGCTAATGGAC
ATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAAGGCGCAAAGGCATACA
TTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAAGAACGCGATAAGCGAT
TGGCACAAAAAACCACTAACTAA
>g13143.t2 Gene=g13143 Length=265
MKHKARGPKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALT
NTETKKIVMQRHIKVDGKVRTDINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITAD
EAKYKLCKVKRVTIGPKKIPYLVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFES
GNLVMVTGGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMFATRLTNIFIIGKGAKAYIS
LPKGKGIKLSVAEERDKRLAQKTTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g13143.t2 | CDD | cd00165 | S4 | 47 | 115 | 2.59165E-6 |
| 14 | g13143.t2 | CDD | cd06087 | KOW_RPS4 | 178 | 232 | 1.73817E-28 |
| 10 | g13143.t2 | Gene3D | G3DSA:3.10.290.40 | - | 4 | 120 | 4.7E-60 |
| 12 | g13143.t2 | Gene3D | G3DSA:2.40.50.740 | - | 125 | 175 | 6.6E-29 |
| 11 | g13143.t2 | Gene3D | G3DSA:2.30.30.30 | - | 178 | 248 | 4.3E-36 |
| 8 | g13143.t2 | Hamap | MF_00485 | 30S ribosomal protein S4e [rps4e]. | 10 | 241 | 36.502556 |
| 6 | g13143.t2 | PANTHER | PTHR11581:SF30 | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | 5 | 262 | 1.8E-137 |
| 7 | g13143.t2 | PANTHER | PTHR11581 | 30S/40S RIBOSOMAL PROTEIN S4 | 5 | 262 | 1.8E-137 |
| 13 | g13143.t2 | PIRSF | PIRSF002116 | RPS4a_RPS4e | 4 | 244 | 1.8E-99 |
| 1 | g13143.t2 | Pfam | PF08071 | RS4NT (NUC023) domain | 6 | 42 | 8.2E-20 |
| 3 | g13143.t2 | Pfam | PF01479 | S4 domain | 46 | 93 | 1.5E-9 |
| 5 | g13143.t2 | Pfam | PF00900 | Ribosomal family S4e | 98 | 172 | 3.4E-36 |
| 2 | g13143.t2 | Pfam | PF00467 | KOW motif | 181 | 213 | 4.3E-6 |
| 4 | g13143.t2 | Pfam | PF16121 | 40S ribosomal protein S4 C-terminus | 215 | 262 | 6.4E-26 |
| 18 | g13143.t2 | ProSitePatterns | PS00528 | Ribosomal protein S4e signature. | 11 | 25 | - |
| 19 | g13143.t2 | ProSiteProfiles | PS50889 | S4 RNA-binding domain profile. | 45 | 108 | 10.755 |
| 16 | g13143.t2 | SMART | SM00363 | s4_6 | 45 | 109 | 2.2E-4 |
| 17 | g13143.t2 | SMART | SM00739 | kow_9 | 177 | 204 | 0.0023 |
| 9 | g13143.t2 | SUPERFAMILY | SSF55174 | Alpha-L RNA-binding motif | 54 | 137 | 2.49E-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