General information for g7976.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S15a.
Parent gene
- The parent gene g7976 is located on chr_2: 27435452..27440035 (+ 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 | g7976 | g7976.t1 | isoform | g7976.t1 | 27434743 | 27435915 |
| chr_2 | g7976 | g7976.t1 | exon | g7976.t1.exon1 | 27434743 | 27434789 |
| chr_2 | g7976 | g7976.t1 | cds | g7976.t1.CDS1 | 27434743 | 27434789 |
| chr_2 | g7976 | g7976.t1 | exon | g7976.t1.exon2 | 27435068 | 27435087 |
| chr_2 | g7976 | g7976.t1 | cds | g7976.t1.CDS2 | 27435068 | 27435087 |
| chr_2 | g7976 | g7976.t1 | exon | g7976.t1.exon3 | 27435453 | 27435750 |
| chr_2 | g7976 | g7976.t1 | cds | g7976.t1.CDS3 | 27435453 | 27435750 |
| chr_2 | g7976 | g7976.t1 | exon | g7976.t1.exon4 | 27435822 | 27435915 |
| chr_2 | g7976 | g7976.t1 | cds | g7976.t1.CDS4 | 27435822 | 27435915 |
| chr_2 | g7976 | g7976.t1 | TTS | g7976.t1 | 27435968 | 27435968 |
| chr_2 | g7976 | g7976.t1 | TSS | g7976.t1 | NA | NA |
Sequences
>g7976.t1 Gene=g7976 Length=459
ATGCTGTGTGATTTTATTCATTCTCTTCTTGTCTTTGTACGTATTGAATACGTGAATTCC
ATAAAAATGGTTCGTGTAAGCGTATTGGCTGATGCCCTCAAATGCATTAATAATGCAGAA
AAACGTGGAAAGCGCCAAGTTTTAATTCGCCCAAATTCCAAAGTTGTCATTAAATTCCTG
ACCGTTATGATGAAACATGGATATATCGGAGAATTCGAGATCGTCGATGACCATCGCGCT
GGAAAAGTAGTTGTTAATCTTACTGGTCGCCTCAATAAAGCTGGTATCATTTCACCCAGA
TTTGACGTTCCAATTCTCGATATTGAAAAGTGGACAAATACACTCCTTCCTTCACGACAG
TTTGGATATGTTGTTTTAACGACAAGTGGTGGAATCATGGACCATGAAGAGGCCCGTAGA
AAACATTTGGGAGGAAAGATTTTGGGATACTTCTTCTAA
>g7976.t1 Gene=g7976 Length=152
MLCDFIHSLLVFVRIEYVNSIKMVRVSVLADALKCINNAEKRGKRQVLIRPNSKVVIKFL
TVMMKHGYIGEFEIVDDHRAGKVVVNLTGRLNKAGIISPRFDVPILDIEKWTNTLLPSRQ
FGYVVLTTSGGIMDHEEARRKHLGGKILGYFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g7976.t1 | Gene3D | G3DSA:3.30.1370.30 | - | 23 | 91 | 4.9E-39 |
| 6 | g7976.t1 | Gene3D | G3DSA:3.30.1490.10 | - | 92 | 152 | 8.0E-31 |
| 2 | g7976.t1 | PANTHER | PTHR11758 | 40S RIBOSOMAL PROTEIN S15A | 23 | 152 | 1.6E-67 |
| 3 | g7976.t1 | PANTHER | PTHR11758:SF34 | - | 23 | 152 | 1.6E-67 |
| 1 | g7976.t1 | Pfam | PF00410 | Ribosomal protein S8 | 29 | 152 | 1.3E-20 |
| 5 | g7976.t1 | ProSitePatterns | PS00053 | Ribosomal protein S8 signature. | 122 | 139 | - |
| 4 | g7976.t1 | SUPERFAMILY | SSF56047 | Ribosomal protein S8 | 26 | 152 | 1.44E-40 |
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 K02957 (small subunit ribosomal protein S15Ae)
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.
