General information for g7115.t195
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S9.
Parent gene
- The parent gene g7115 is located on chr_2: 21264902..21266725 (- 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 | g7115 | g7115.t195 | TTS | g7115.t195 | 21263047 | 21263047 |
| chr_2 | g7115 | g7115.t195 | isoform | g7115.t195 | 21263156 | 21264902 |
| chr_2 | g7115 | g7115.t195 | exon | g7115.t195.exon1 | 21263156 | 21263272 |
| chr_2 | g7115 | g7115.t195 | cds | g7115.t195.CDS1 | 21263268 | 21263272 |
| chr_2 | g7115 | g7115.t195 | exon | g7115.t195.exon2 | 21263791 | 21263831 |
| chr_2 | g7115 | g7115.t195 | cds | g7115.t195.CDS2 | 21263791 | 21263831 |
| chr_2 | g7115 | g7115.t195 | exon | g7115.t195.exon3 | 21264028 | 21264446 |
| chr_2 | g7115 | g7115.t195 | cds | g7115.t195.CDS3 | 21264028 | 21264437 |
| chr_2 | g7115 | g7115.t195 | exon | g7115.t195.exon4 | 21264852 | 21264902 |
| chr_2 | g7115 | g7115.t195 | TSS | g7115.t195 | 21264887 | 21264887 |
Sequences
>g7115.t195 Gene=g7115 Length=628
CGCGATTTTCTCTTTCTTTTCGAAAAATTCTTGCAAAAAGAATTTTGTCAAGTTTTCATC
ATGGTTAATCACAGAATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAGACGTCCA
TATGAAAAACCTCGCTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCTCCGTAAC
AAGCGTGAGGTATGGCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGCTCGTGAA
TTGCTTACACTTGAAGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCTTCTTCGT
CGTCTTGTTCGTATTGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGTTCTTGGT
TTAAAAATTGAAGATTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACTCGGTTTG
GCTAAATCTTATCATCATGCTCGCGTTCTTATCCGACAAAGACATATTCGCGTTCGTAAA
CAAGTCGTCAACATCCCATCATTTGTCGTTCATTGATTTCTCATTGAAGTCACCATTCGG
TGGTGGACGACCAGGTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGG
TGGCGCTGATGAAGAAGAAGAGGATTAA
>g7115.t195 Gene=g7115 Length=151
MVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFGLRNKREVWRVKYTLAKIRKAARE
LLTLEEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL
AKSYHHARVLIRQRHIRVRKQVVNIPSFVVH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g7115.t195 | CDD | cd00165 | S4 | 109 | 150 | 9.77295E-6 |
| 5 | g7115.t195 | Gene3D | G3DSA:3.10.290.10 | - | 110 | 150 | 3.9E-10 |
| 2 | g7115.t195 | PANTHER | PTHR11831:SF23 | 40S RIBOSOMAL PROTEIN S9 | 8 | 150 | 3.5E-73 |
| 3 | g7115.t195 | PANTHER | PTHR11831 | 30S 40S RIBOSOMAL PROTEIN | 8 | 150 | 3.5E-73 |
| 1 | g7115.t195 | Pfam | PF01479 | S4 domain | 109 | 150 | 4.4E-9 |
| 7 | g7115.t195 | ProSitePatterns | PS00632 | Ribosomal protein S4 signature. | 107 | 131 | - |
| 8 | g7115.t195 | SMART | SM01390 | Ribosomal_S4_2 | 4 | 108 | 2.3E-17 |
| 4 | g7115.t195 | SUPERFAMILY | SSF55174 | Alpha-L RNA-binding motif | 12 | 150 | 1.82E-32 |
| 9 | g7115.t195 | TIGRFAM | TIGR01018 | uS4_arch: ribosomal protein uS4 | 11 | 150 | 6.3E-60 |
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:0003723 | RNA binding | MF |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
| GO:0015935 | small ribosomal subunit | CC |
| GO:0019843 | rRNA binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
