General information for g5690.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable 28S ribosomal protein S16, mitochondrial.
Parent gene
- The parent gene g5690 is located on chr_2: 11259984..11260467 (- 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 | g5690 | g5690.t1 | TTS | g5690.t1 | 11259916 | 11259916 |
| chr_2 | g5690 | g5690.t1 | isoform | g5690.t1 | 11259984 | 11260467 |
| chr_2 | g5690 | g5690.t1 | exon | g5690.t1.exon1 | 11259984 | 11260244 |
| chr_2 | g5690 | g5690.t1 | cds | g5690.t1.CDS1 | 11259984 | 11260244 |
| chr_2 | g5690 | g5690.t1 | exon | g5690.t1.exon2 | 11260303 | 11260467 |
| chr_2 | g5690 | g5690.t1 | cds | g5690.t1.CDS2 | 11260303 | 11260467 |
| chr_2 | g5690 | g5690.t1 | TSS | g5690.t1 | 11260520 | 11260520 |
Sequences
>g5690.t1 Gene=g5690 Length=426
ATGGCAAGTAAAGCGTTTGAAAATGTTAAAATGCTTCCTCGTATTAGGAATGCATTGTCA
CCAGCATCAGGAACTGGTCAATTTTATGAAAGATCAGCAAAGAGCATTCGTCTTTTCAAA
CAAGGCTGCACAAATAGACCATTCTTTCAAATTGTTGTTATGGAGCGCCGAAAACCACAC
TATGAACCAGTGATTGAGCAAGTGGGAACTTACGATCCAATGCCAAATAAATATAATCAA
ATTATGGTTTCATTCAATTATGAACGTATAAGGCACTGGATTGGTCATGGAGCACACATT
TCAACACCTGTATTAGAGCTATTAGGATTATCGGGATTTTATCCCATTTATCCTAAAACC
TACATGAAAGCATGGCGAGCAAGAGCGACTGAAGCAAAAAAAGAGACAGTTCAAGAAAGT
TCATAA
>g5690.t1 Gene=g5690 Length=141
MASKAFENVKMLPRIRNALSPASGTGQFYERSAKSIRLFKQGCTNRPFFQIVVMERRKPH
YEPVIEQVGTYDPMPNKYNQIMVSFNYERIRHWIGHGAHISTPVLELLGLSGFYPIYPKT
YMKAWRARATEAKKETVQESS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5690.t1 | Gene3D | G3DSA:3.30.1320.10 | - | 22 | 141 | 0.00000 |
| 4 | g5690.t1 | Hamap | MF_00385 | 30S ribosomal protein S16 [rpsP]. | 33 | 111 | 17.46296 |
| 2 | g5690.t1 | PANTHER | PTHR12919:SF27 | 28S RIBOSOMAL PROTEIN S16, MITOCHONDRIAL | 28 | 139 | 0.00000 |
| 3 | g5690.t1 | PANTHER | PTHR12919 | 30S RIBOSOMAL PROTEIN S16 | 28 | 139 | 0.00000 |
| 1 | g5690.t1 | Pfam | PF00886 | Ribosomal protein S16 | 41 | 101 | 0.00000 |
| 5 | g5690.t1 | SUPERFAMILY | SSF54565 | Ribosomal protein S16 | 35 | 134 | 0.00000 |
| 7 | g5690.t1 | TIGRFAM | TIGR00002 | S16: ribosomal protein bS16 | 36 | 112 | 0.00000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5690/g5690.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5690.t1.fa.iupred3.txt does not exist
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 K02959 (small subunit ribosomal protein S16)
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.
