General information for g556.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S16.
Parent gene
- The parent gene g556 is located on chr_3: 4038505..4046543 (+ 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 | g556 | g556.t2 | isoform | g556.t2 | 4037429 | 4038951 |
| chr_3 | g556 | g556.t2 | exon | g556.t2.exon1 | 4037429 | 4037571 |
| chr_3 | g556 | g556.t2 | exon | g556.t2.exon2 | 4038498 | 4038951 |
| chr_3 | g556 | g556.t2 | cds | g556.t2.CDS1 | 4038505 | 4038951 |
| chr_3 | g556 | g556.t2 | TTS | g556.t2 | 4039072 | 4039072 |
| chr_3 | g556 | g556.t2 | TSS | g556.t2 | NA | NA |
Sequences
>g556.t2 Gene=g556 Length=597
TAATTTTTTTAGTTTTTATCACTGAATGCTGCTTCTTAAATTTCCCAAATAATACTGAAA
ACATCAGAGATTTAACTATGTGTATTTATTCAAATCATCATTGCGTTGTATTAAGAGAAG
AAATACACTAATTGAATGAGAATATACAAAATGCCGAAAAAAGTCAAAGAACCAGTTAAC
GCAGTGCATGTTTTCGGACGCAAGAAGACAGCAATCGCTACTGCTTATTGCAAGAGAGGT
CGTGGTCTTTTGCGAGTGAATGGACGTCCTTTGGAGCAGATTGAACCGAAAATTTTGCAA
TCAAAATTGCAAGAACCATTGCTTTTGTTGGGCAAAGAAAAATTCTCCGGAATTGATATT
CGTGTCCGAGTCTCTGGCGGTGGTCAAGTAGCACAAATCTATGCTATTCGTCAGGCAATT
TCAAGAGCCATCGTCTCATTCTATCAAAAGTATGTCGATGAAGCATCTCGTAAAGAACTT
AAAGACATCTTGACACAATACGACAGAACATTGCTCGTTGCTGACCCAAGACGTTGCGAG
CCAAAGAAATTCGGCGGTCCCGGTGCTCGTGCTCGCTATCAAAAATCATACCGTTAA
>g556.t2 Gene=g556 Length=148
MPKKVKEPVNAVHVFGRKKTAIATAYCKRGRGLLRVNGRPLEQIEPKILQSKLQEPLLLL
GKEKFSGIDIRVRVSGGGQVAQIYAIRQAISRAIVSFYQKYVDEASRKELKDILTQYDRT
LLVADPRRCEPKKFGGPGARARYQKSYR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g556.t2 | Gene3D | G3DSA:3.30.230.10 | - | 3 | 148 | 4.5E-68 |
| 2 | g556.t2 | PANTHER | PTHR21569:SF15 | 40S RIBOSOMAL PROTEIN S16 | 5 | 148 | 6.8E-74 |
| 3 | g556.t2 | PANTHER | PTHR21569 | RIBOSOMAL PROTEIN S9 | 5 | 148 | 6.8E-74 |
| 1 | g556.t2 | Pfam | PF00380 | Ribosomal protein S9/S16 | 16 | 148 | 4.4E-34 |
| 5 | g556.t2 | ProSitePatterns | PS00360 | Ribosomal protein S9 signature. | 76 | 94 | - |
| 4 | g556.t2 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 12 | 148 | 6.07E-39 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g556/g556.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g556.t2.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 K02960 (small subunit ribosomal protein S16e)
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. There were no conditions that were differentially expressed