General information for g11474.t29
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.t29 | TTS | g11474.t29 | 16437300 | 16437300 |
| chr_1 | g11474 | g11474.t29 | isoform | g11474.t29 | 16437372 | 16438953 |
| chr_1 | g11474 | g11474.t29 | exon | g11474.t29.exon1 | 16437372 | 16437863 |
| chr_1 | g11474 | g11474.t29 | cds | g11474.t29.CDS1 | 16437372 | 16437863 |
| chr_1 | g11474 | g11474.t29 | exon | g11474.t29.exon2 | 16437937 | 16438286 |
| chr_1 | g11474 | g11474.t29 | cds | g11474.t29.CDS2 | 16437937 | 16438286 |
| chr_1 | g11474 | g11474.t29 | exon | g11474.t29.exon3 | 16438516 | 16438953 |
| chr_1 | g11474 | g11474.t29 | cds | g11474.t29.CDS3 | 16438516 | 16438633 |
| chr_1 | g11474 | g11474.t29 | TSS | g11474.t29 | 16438988 | 16438988 |
Sequences
>g11474.t29 Gene=g11474 Length=1280
ATGAAGGTGAATAAATTAAAAATTCTAAGATAAATCTTGAAATTCAATTGAAATGATATT
TTCATAATAAGTATAAGTGTTTAATGAATGAAAAACACTCAAAATATTGCACAGAAATAC
ACAAAATTAATAAATAATTGTGAAAATATTTTTTCCCGATGTTAAAAAATTCTTCCATGT
GTATATTGTATTGAAAAATTCTAATGGTTTTTTATTTTTCTATTTTATTTTAGTTAAACG
TCTCCTATCCCTCAACGGGAGCTCAGAAAACTTTTGAGGTCAACGATGACCACAAATTGC
GATTGTTTTACGAGAAACGCATGGGCGCTGAAATTGAAGCTGATCAATTAGGCGATGAAT
GGAAAGGATATATTCTTAAAATCGCTGGTGGTAATGATAAACAAGGTTTCCCAATGAAAC
AGGGTGTTTTAACAAACACTCGTGTTCGTCTCTTGCTTAAAAAAGGACATTCCTGTTATC
GTCCAAGAAGAACTGGAGAACGTAAACGTAAATCAGTTCGTGGTTGCATTGTTGATCAAA
ACTTGTCAGCTCTCGCTTTGATCGTCGTACGTAAGGGTGAGAGTGAAGTTGAAGGTTTAA
CTGATGTCACCGTTCCTCGTCGTCTCGGACCTAAACGTGCAAGCCACATTCGTAAACTGT
TTGCTTTGACAAAAGAGGATGATGTTCGCAAGTATGTCATTAAGAAGCCTTTGCCACCAA
AAGAGGGCAAAAAGCAACGTTTTCAAGCTCCTAGAATTCAACGTTTAGTAACACCGGTCG
TTTTACAGCGTAAAAGACATCGTTTGGCTCTTAAAAAACGCCGAGTTGAATCACGCAAAG
AAGCTGAAGCTGAATATGCAAAATTATTAGCTCAGCGTAGACGTGAAGAAAAACTTCGTC
GTCGTACACGTTCAGCATCTATTCGTGAATCAAAGAGCTCAATTTCATCAGATAAAGATA
GCAAGAAAGAAGTTAAGAAGCCAGAAGTTGTCAAGAAAGTTGAAGCTAAACCAGCAAAGA
AGGTTGAAGAGAAGAAAAAGGTTGATGACAAAAAGAAACCAGCTGAAAAGAAAGTTGAAA
CTAAAAAGGGTGATGCAAAAGCCGCCGCTGTAAAGAAGATTGAAGAAAAGAAAAAGCCAG
CCCAAGCTGAGAAGAAATCTGCAGACAAAAAACCAGCAGCTGCACCAGCAAAGAAAGAGG
CCCCAAAGCCTGCAACAGCACCATCAGCCAAGAAGGAAGCATCTAAACCAACAGATGCAA
AGAAGCCCAAAAAAAAGTAA
>g11474.t29 Gene=g11474 Length=319
MGAEIEADQLGDEWKGYILKIAGGNDKQGFPMKQGVLTNTRVRLLLKKGHSCYRPRRTGE
RKRKSVRGCIVDQNLSALALIVVRKGESEVEGLTDVTVPRRLGPKRASHIRKLFALTKED
DVRKYVIKKPLPPKEGKKQRFQAPRIQRLVTPVVLQRKRHRLALKKRRVESRKEAEAEYA
KLLAQRRREEKLRRRTRSASIRESKSSISSDKDSKKEVKKPEVVKKVEAKPAKKVEEKKK
VDDKKKPAEKKVETKKGDAKAAAVKKIEEKKKPAQAEKKSADKKPAAAPAKKEAPKPATA
PSAKKEASKPTDAKKPKKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11474.t29 | Coils | Coil | Coil | 172 | 192 | - |
| 6 | g11474.t29 | MobiDBLite | mobidb-lite | consensus disorder prediction | 187 | 319 | - |
| 7 | g11474.t29 | MobiDBLite | mobidb-lite | consensus disorder prediction | 187 | 290 | - |
| 2 | g11474.t29 | PANTHER | PTHR11502:SF6 | 40S RIBOSOMAL PROTEIN S6 | 1 | 214 | 2.7E-99 |
| 3 | g11474.t29 | PANTHER | PTHR11502 | 40S RIBOSOMAL PROTEIN S6 | 1 | 214 | 2.7E-99 |
| 1 | g11474.t29 | Pfam | PF01092 | Ribosomal protein S6e | 1 | 95 | 2.3E-44 |
| 5 | g11474.t29 | ProSitePatterns | PS00578 | Ribosomal protein S6e signature. | 21 | 32 | - |
| 4 | g11474.t29 | SMART | SM01405 | Ribosomal_S6e_2 | 1 | 95 | 2.9E-50 |
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.
