General information for g11474.t39
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S6.
Parent gene
- The parent gene g11474 is located on chr_1: 16438523..16438986 (- 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 | g11474 | g11474.t39 | TTS | g11474.t39 | 16437300 | 16437300 |
| chr_1 | g11474 | g11474.t39 | isoform | g11474.t39 | 16437372 | 16438953 |
| chr_1 | g11474 | g11474.t39 | exon | g11474.t39.exon1 | 16437372 | 16437472 |
| chr_1 | g11474 | g11474.t39 | cds | g11474.t39.CDS1 | 16437374 | 16437472 |
| chr_1 | g11474 | g11474.t39 | exon | g11474.t39.exon2 | 16437612 | 16437863 |
| chr_1 | g11474 | g11474.t39 | cds | g11474.t39.CDS2 | 16437612 | 16437863 |
| chr_1 | g11474 | g11474.t39 | exon | g11474.t39.exon3 | 16437937 | 16438286 |
| chr_1 | g11474 | g11474.t39 | cds | g11474.t39.CDS3 | 16437937 | 16438286 |
| chr_1 | g11474 | g11474.t39 | exon | g11474.t39.exon4 | 16438516 | 16438720 |
| chr_1 | g11474 | g11474.t39 | cds | g11474.t39.CDS4 | 16438516 | 16438720 |
| chr_1 | g11474 | g11474.t39 | exon | g11474.t39.exon5 | 16438948 | 16438953 |
| chr_1 | g11474 | g11474.t39 | cds | g11474.t39.CDS5 | 16438948 | 16438953 |
| chr_1 | g11474 | g11474.t39 | TSS | g11474.t39 | 16438988 | 16438988 |
Sequences
>g11474.t39 Gene=g11474 Length=914
ATGAAGTTAAACGTCTCCTATCCCTCAACGGGAGCTCAGAAAACTTTTGAGGTCAACGAT
GACCACAAATTGCGATTGTTTTACGAGAAACGCATGGGCGCTGAAATTGAAGCTGATCAA
TTAGGCGATGAATGGAAAGGATATATTCTTAAAATCGCTGGTGGTAATGATAAACAAGGT
TTCCCAATGAAACAGGGTGTTTTAACAAACACTCGTGTTCGTCTCTTGCTTAAAAAAGGA
CATTCCTGTTATCGTCCAAGAAGAACTGGAGAACGTAAACGTAAATCAGTTCGTGGTTGC
ATTGTTGATCAAAACTTGTCAGCTCTCGCTTTGATCGTCGTACGTAAGGGTGAGAGTGAA
GTTGAAGGTTTAACTGATGTCACCGTTCCTCGTCGTCTCGGACCTAAACGTGCAAGCCAC
ATTCGTAAACTGTTTGCTTTGACAAAAGAGGATGATGTTCGCAAGTATGTCATTAAGAAG
CCTTTGCCACCAAAAGAGGGCAAAAAGCAACGTTTTCAAGCTCCTAGAATTCAACGTTTA
GTAACACCGGTCGTTTTACAGCGTAAAAGACATCGTTTGGCTCTTAAAAAACGCCGAGTT
GAATCACGCAAAGAAGCTGAAGCTGAATATGCAAAATTATTAGCTCAGCGTAGACGTGAA
GAAAAACTTCGTCGTCGTACACGTTCAGCATCTATTCGTGAATCAAAGAGCTCAATTTCA
TCAGATAAAGATAGCAAGAAAGAAGTTAAGAAGCCAGAAGTTGTCAAGAAAGTTGAAGCT
AAACCAGCAAAGAAGGTTGAAGAGAAGAAAAAGCTGCACCAGCAAAGAAAGAGGCCCCAA
AGCCTGCAACAGCACCATCAGCCAAGAAGGAAGCATCTAAACCAACAGATGCAAAGAAGC
CCAAAAAAAAGTAA
>g11474.t39 Gene=g11474 Length=304
MKLNVSYPSTGAQKTFEVNDDHKLRLFYEKRMGAEIEADQLGDEWKGYILKIAGGNDKQG
FPMKQGVLTNTRVRLLLKKGHSCYRPRRTGERKRKSVRGCIVDQNLSALALIVVRKGESE
VEGLTDVTVPRRLGPKRASHIRKLFALTKEDDVRKYVIKKPLPPKEGKKQRFQAPRIQRL
VTPVVLQRKRHRLALKKRRVESRKEAEAEYAKLLAQRRREEKLRRRTRSASIRESKSSIS
SDKDSKKEVKKPEVVKKVEAKPAKKVEEKKKLHQQRKRPQSLQQHHQPRRKHLNQQMQRS
PKKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11474.t39 | Coils | Coil | Coil | 203 | 223 | - |
| 6 | g11474.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 218 | 269 | - |
| 7 | g11474.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 218 | 304 | - |
| 5 | g11474.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 270 | 304 | - |
| 2 | g11474.t39 | PANTHER | PTHR11502 | 40S RIBOSOMAL PROTEIN S6 | 1 | 245 | 1.5E-115 |
| 1 | g11474.t39 | Pfam | PF01092 | Ribosomal protein S6e | 1 | 126 | 4.3E-59 |
| 4 | g11474.t39 | ProSitePatterns | PS00578 | Ribosomal protein S6e signature. | 52 | 63 | - |
| 3 | g11474.t39 | SMART | SM01405 | Ribosomal_S6e_2 | 1 | 126 | 4.9E-83 |
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 K02991 (small subunit ribosomal protein S6e)
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.
