General information for g4086.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S8.
Parent gene
- The parent gene g4086 is located on chr_3: 30509687..30510484 (- 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_3 | g4086 | g4086.t12 | TTS | g4086.t12 | 30509274 | 30509274 |
| chr_3 | g4086 | g4086.t12 | isoform | g4086.t12 | 30509347 | 30510318 |
| chr_3 | g4086 | g4086.t12 | exon | g4086.t12.exon1 | 30509347 | 30509456 |
| chr_3 | g4086 | g4086.t12 | cds | g4086.t12.CDS1 | 30509347 | 30509456 |
| chr_3 | g4086 | g4086.t12 | exon | g4086.t12.exon2 | 30509682 | 30510093 |
| chr_3 | g4086 | g4086.t12 | cds | g4086.t12.CDS2 | 30509682 | 30510093 |
| chr_3 | g4086 | g4086.t12 | exon | g4086.t12.exon3 | 30510269 | 30510318 |
| chr_3 | g4086 | g4086.t12 | cds | g4086.t12.CDS3 | 30510269 | 30510316 |
| chr_3 | g4086 | g4086.t12 | TSS | g4086.t12 | 30510508 | 30510508 |
Sequences
>g4086.t12 Gene=g4086 Length=572
TATTTCTCGCGATTCATTTCATAAACGCCGTGCGACTGGAGGCAAGAAGGATCGGCGCTC
ATCGCGTACATTTTGTAAGAACCCGTGGTGGTAACAGAAAATTCCGTGCCCTTCGTTTAG
ACGGTGGTAATTTTGCATGGGCTTCACAAGGAGCTGCACGCAAAACTAGAATTCTCGATG
TCGTCTACAATGCATCAAACAACGAACTCGTTCGTACAAAGACATTGGTAAAGAATTGCA
TTGTTTCCATTGATGCTACACCATTCAAGCAGTTCTACGAAAGTCATTACTTGCTTCCAC
TTGGTCGCAAGAAGGATCACAAAGTGCAACTTGCAGAAGGTGAGGAAGATCCACTGACAA
AGAAACGTAGCAAAGATGCATTGAAGAAATACGAAGAACGTCAAAAGTATGCTAAAGTTG
AACCAGCTTTAGAAGAACAATTCTTGCAAGGACGTTTATTAGCTGCTATCTCAAGCAGAC
CAGGACAATGTGGTCGTGCTGATGGATATATTTTGGAAGGCAAGGAACTCGAGTTCTACG
TTAAGAAAATCAAATCTAAGAAATCAAAGTAA
>g4086.t12 Gene=g4086 Length=189
FLAIHFINAVRLEARRIGAHRVHFVRTRGGNRKFRALRLDGGNFAWASQGAARKTRILDV
VYNASNNELVRTKTLVKNCIVSIDATPFKQFYESHYLLPLGRKKDHKVQLAEGEEDPLTK
KRSKDALKKYEERQKYAKVEPALEEQFLQGRLLAAISSRPGQCGRADGYILEGKELEFYV
KKIKSKKSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4086.t12 | CDD | cd11380 | Ribosomal_S8e_like | 18 | 171 | 0 |
| 4 | g4086.t12 | Gene3D | G3DSA:2.40.10.450 | - | 5 | 103 | 0 |
| 5 | g4086.t12 | Gene3D | G3DSA:2.40.10.450 | - | 104 | 188 | 0 |
| 2 | g4086.t12 | PANTHER | PTHR10394 | 40S RIBOSOMAL PROTEIN S8 | 16 | 189 | 0 |
| 3 | g4086.t12 | PANTHER | PTHR10394:SF3 | 40S RIBOSOMAL PROTEIN S8 | 16 | 189 | 0 |
| 1 | g4086.t12 | Pfam | PF01201 | Ribosomal protein S8e | 14 | 171 | 0 |
| 6 | g4086.t12 | TIGRFAM | TIGR00307 | eS8: ribosomal protein eS8 | 16 | 173 | 0 |
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.
