General information for g1175.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 28S ribosomal protein S11, mitochondrial.
Parent gene
- The parent gene g1175 is located on chr_3: 8489656..8492512 (- 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 | g1175 | g1175.t28 | isoform | g1175.t28 | 8488913 | 8489464 |
| chr_3 | g1175 | g1175.t28 | exon | g1175.t28.exon1 | 8488913 | 8489464 |
| chr_3 | g1175 | g1175.t28 | TTS | g1175.t28 | 8488936 | 8488936 |
| chr_3 | g1175 | g1175.t28 | cds | g1175.t28.CDS1 | 8489004 | 8489357 |
| chr_3 | g1175 | g1175.t28 | TSS | g1175.t28 | 8489682 | 8489682 |
Sequences
>g1175.t28 Gene=g1175 Length=552
TGAGGAAAAAATATGGTAATATATTTACGAAATATTTAGTCTGTTTAAATTGCAGTAAAA
TTGATATATTTCCTGATGAAAACACACCAAATGCTATTTTCTATGATATGCCTTTCAAGG
AATTGCCAATTGTGAATATTCGTGTGTCAAAAAATAATACTATATTATCGCTAACAAATT
CAAAAGGCGTTATTCAAATGATTCGATCTTGTGGTGTTGAGGGTTTCAAAAATACGAGAA
AAGGAACAAATATTGCTGCTCAAGCGACAGCAATTACTTTTTGCGGAAAAGTTATTGATA
GAGGCATTAAAGCTGCTAGAATTGTTGTGAGAGGCTTAGGACCAGGACGTATGTCAGCTA
TAAAAGGGTTACAAATGGGAGGATTAAATATTGTCTCAATTACTGATACGACTCGAGTTA
GTTGGAGCGGTCCTCGTCCAAGAAAACAAAGAAAGTTATAAATATTCATTATTCTTCATT
ATTATAAGTTTATTTAGAAAGAAAGAAAAAAAATATAAGTCTCATTGACAAAAAAAAAAT
TATAGAAAATCT
>g1175.t28 Gene=g1175 Length=117
MPFKELPIVNIRVSKNNTILSLTNSKGVIQMIRSCGVEGFKNTRKGTNIAAQATAITFCG
KVIDRGIKAARIVVRGLGPGRMSAIKGLQMGGLNIVSITDTTRVSWSGPRPRKQRKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1175.t28 | Gene3D | G3DSA:3.30.420.80 | - | 1 | 117 | 0.0000 |
| 4 | g1175.t28 | Hamap | MF_01310 | 30S ribosomal protein S11 [rpsK]. | 4 | 117 | 18.8648 |
| 2 | g1175.t28 | PANTHER | PTHR11759 | 40S RIBOSOMAL PROTEIN S14/30S RIBOSOMAL PROTEIN S11 | 2 | 117 | 0.0000 |
| 3 | g1175.t28 | PANTHER | PTHR11759:SF3 | 28S RIBOSOMAL PROTEIN S11, MITOCHONDRIAL | 2 | 117 | 0.0000 |
| 7 | g1175.t28 | PIRSF | PIRSF002131 | RPS11p_RPS11a_RPS14e_RPS11o | 2 | 117 | 0.0000 |
| 1 | g1175.t28 | Pfam | PF00411 | Ribosomal protein S11 | 8 | 116 | 0.0000 |
| 5 | g1175.t28 | SUPERFAMILY | SSF53137 | Translational machinery components | 4 | 117 | 0.0000 |
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 K02948 (small subunit ribosomal protein S11)
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.
