General information for g11504.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g11504 is located on chr_1: 16675990..16676286 (+ 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 | g11504 | g11504.t1 | isoform | g11504.t1 | 16675990 | 16676286 |
| chr_1 | g11504 | g11504.t1 | exon | g11504.t1.exon1 | 16675990 | 16676125 |
| chr_1 | g11504 | g11504.t1 | cds | g11504.t1.CDS1 | 16675990 | 16676125 |
| chr_1 | g11504 | g11504.t1 | exon | g11504.t1.exon2 | 16676195 | 16676286 |
| chr_1 | g11504 | g11504.t1 | cds | g11504.t1.CDS2 | 16676195 | 16676286 |
| chr_1 | g11504 | g11504.t1 | TTS | g11504.t1 | 16676345 | 16676345 |
| chr_1 | g11504 | g11504.t1 | TSS | g11504.t1 | NA | NA |
Sequences
>g11504.t1 Gene=g11504 Length=228
ATGTTAGAAAAAGTTGATATTGAAGCAAATGTTGAAGGTGGTGGTTCATCTGGTCAAGCG
GGTGCAATACGATGGGGTATATCAATGGCATTAAGAAGCTTTGTTGACTCTGAGATGGTT
GAAAAGATGAGATATGCCGGTTTACTTCAGCGTGATTACCGCACTAAAGAAAGAAAGAAG
CCAGGTCAAGAAGGTGCTCGTAGAAAATTCACATGGAAGAAACGATAA
>g11504.t1 Gene=g11504 Length=75
MLEKVDIEANVEGGGSSGQAGAIRWGISMALRSFVDSEMVEKMRYAGLLQRDYRTKERKK
PGQEGARRKFTWKKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11504.t1 | Gene3D | G3DSA:3.30.230.10 | - | 1 | 75 | 1.4E-26 |
| 5 | g11504.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 56 | 75 | - |
| 2 | g11504.t1 | PANTHER | PTHR21569:SF1 | 28S RIBOSOMAL PROTEIN S9, MITOCHONDRIAL | 2 | 75 | 1.7E-27 |
| 3 | g11504.t1 | PANTHER | PTHR21569 | RIBOSOMAL PROTEIN S9 | 2 | 75 | 1.7E-27 |
| 1 | g11504.t1 | Pfam | PF00380 | Ribosomal protein S9/S16 | 2 | 75 | 2.7E-24 |
| 4 | g11504.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 2 | 75 | 2.77E-21 |
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 K02996 (small subunit ribosomal protein S9)
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.
