General information for g8349.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 28S ribosomal protein S15, mitochondrial.
Parent gene
- The parent gene g8349 is located on chr_2: 29891351..29892302 (+ 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_2 | g8349 | g8349.t1 | TSS | g8349.t1 | 29891320 | 29891320 |
| chr_2 | g8349 | g8349.t1 | isoform | g8349.t1 | 29891351 | 29892302 |
| chr_2 | g8349 | g8349.t1 | exon | g8349.t1.exon1 | 29891351 | 29891738 |
| chr_2 | g8349 | g8349.t1 | cds | g8349.t1.CDS1 | 29891351 | 29891738 |
| chr_2 | g8349 | g8349.t1 | exon | g8349.t1.exon2 | 29891791 | 29892302 |
| chr_2 | g8349 | g8349.t1 | cds | g8349.t1.CDS2 | 29891791 | 29892302 |
| chr_2 | g8349 | g8349.t1 | TTS | g8349.t1 | 29892350 | 29892350 |
Sequences
>g8349.t1 Gene=g8349 Length=900
ATGCTTAAAAAATTTTCAAAATTACTTTTCTTCAAAAATCAGCTCACTCCATTGCTGATC
ACAGTTAGAAATTATCCTAAGTTTAAAGGAGGAAAACCTGCAATGAAGCATGAAGTTTTT
GATTACATTAAATGGGTACGTCCACAAAAAATTCCAACAATTGATCCTGAAAAAAGTGGC
GATTTAGCTTCAATGCCGAAATATGATTTGAAGCAGTCTTTACTTTATTTTGATAACTCT
TCATTATTGGAAAATGCTAACGAATTAGTCAAGTCAAAATTCACACTAGAACTGAATCCA
GGAAAAGAAGAGAAAGCATTGTATAAAGAGGAGTTAGTGAAGAAAGTTCAGAGACACGAT
CAAGATTATGGCTCAATGGAAGCTAAATTGGCAAAAATGACAGCAATCATTCGATATTGG
CAAGTTCGATTAAAGGAAAATCCTAAAAATTCAAGACTCAAGACGTTAACAAAAGAACTC
ATTGAGAAGAGAAAAAAATATTTGAAATTTTTACGTCGAGATGATTACAAGAGGTTTGAA
TATATACTCGAACAATTAGAATTGAAATATGTCCCATATCCAAATAAATTTCACTGGATA
GCAAGAAAAGAAGCAATGAGAGCTTTGACAAAAAGATTCTGTCGAGGCATTCAAATTGAA
AGATTGAAAGAATACAAAGCGACACTTCAAGCACAACAGCTTGATTTCTTAGAGAATAAA
ATCAAAAACTTGGAATTCATTAGAAATGAGCAAATTGAATGCAAAGTTCCAGTGACAGTC
ACAAATGAAGAAATTAATGCAGTTAAGAAACAATATAAAGAGCTGAAACAGCAGAGAGAT
GAAGAAGCTGAAATTCGAAGAAAGAATGAAGTAAGAGACGATTACGAAATTAAATTGTAA
>g8349.t1 Gene=g8349 Length=299
MLKKFSKLLFFKNQLTPLLITVRNYPKFKGGKPAMKHEVFDYIKWVRPQKIPTIDPEKSG
DLASMPKYDLKQSLLYFDNSSLLENANELVKSKFTLELNPGKEEKALYKEELVKKVQRHD
QDYGSMEAKLAKMTAIIRYWQVRLKENPKNSRLKTLTKELIEKRKKYLKFLRRDDYKRFE
YILEQLELKYVPYPNKFHWIARKEAMRALTKRFCRGIQIERLKEYKATLQAQQLDFLENK
IKNLEFIRNEQIECKVPVTVTNEEINAVKKQYKELKQQRDEEAEIRRKNEVRDDYEIKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8349.t1 | Coils | Coil | Coil | 258 | 288 | - |
| 5 | g8349.t1 | Gene3D | G3DSA:1.10.287.10 | - | 105 | 189 | 5.7E-15 |
| 2 | g8349.t1 | PANTHER | PTHR46685 | 28S RIBOSOMAL PROTEIN S15, MITOCHONDRIAL | 21 | 264 | 8.0E-51 |
| 1 | g8349.t1 | Pfam | PF00312 | Ribosomal protein S15 | 109 | 188 | 4.2E-16 |
| 4 | g8349.t1 | SMART | SM01387 | Ribosomal_S15_2 | 109 | 189 | 2.6E-8 |
| 3 | g8349.t1 | SUPERFAMILY | SSF47060 | S15/NS1 RNA-binding domain | 107 | 189 | 2.44E-16 |
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 K02956 (small subunit ribosomal protein S15)
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.
