General information for g9524.t55
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S2.
Parent gene
- The parent gene g9524 is located on chr_1: 3889012..3890129 (- 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 | g9524 | g9524.t55 | TTS | g9524.t55 | 3888292 | 3888292 |
| chr_1 | g9524 | g9524.t55 | isoform | g9524.t55 | 3888875 | 3889977 |
| chr_1 | g9524 | g9524.t55 | exon | g9524.t55.exon1 | 3888875 | 3889289 |
| chr_1 | g9524 | g9524.t55 | cds | g9524.t55.CDS1 | 3888877 | 3889289 |
| chr_1 | g9524 | g9524.t55 | exon | g9524.t55.exon2 | 3889490 | 3889611 |
| chr_1 | g9524 | g9524.t55 | cds | g9524.t55.CDS2 | 3889490 | 3889610 |
| chr_1 | g9524 | g9524.t55 | exon | g9524.t55.exon3 | 3889961 | 3889977 |
| chr_1 | g9524 | g9524.t55 | TSS | g9524.t55 | 3890000 | 3890000 |
Sequences
>g9524.t55 Gene=g9524 Length=554
CAAAAGACACGAAAGATAATGGCGGACACAGCTCCAGCCCGTGGTGGGTTTAAACAAGGT
TTCGGAGGTGCAGCTGGTGGTGGTACCGGCGGTGGTGGATCACGAGGAAGAGGTCGACGC
GGAGGTCGCGGTGGAAGAGGTCGTGGCGGACGTGGACGAGGTGACAAAGAAGGAAATCAA
AAAGAATGGGTACCAGTCACTAAATTGGGTCGTTTAGTTCGTGATGGAAAGATTCGTTCA
TTGGAAGAAATTTACTTGTACTCATTGCCAATCAAAGAATTCGAAATCATTGATTTCTTC
TTGGGACGTTCATTGCGTGATGAGGTTTTGAAGATCATGCCTGTTCAGAAACAAACACGT
GCCGGTCAACGTACGCGCTTCAAGGCTTTCGTTGCTATCGGTGATTCAAACGGTCACATT
GGTCTTGGTGTAAAATGCAGCAAAGAAGTCGCCACTGCTATTCGTGGAGCTATCATTTTG
GCTAAACTTTCAGTAGTTCCGGTTCGTCGTGGTTATTGGGGTAACAAAATCGGTAAACCT
CATACAGTACCTTG
>g9524.t55 Gene=g9524 Length=178
MADTAPARGGFKQGFGGAAGGGTGGGGSRGRGRRGGRGGRGRGGRGRGDKEGNQKEWVPV
TKLGRLVRDGKIRSLEEIYLYSLPIKEFEIIDFFLGRSLRDEVLKIMPVQKQTRAGQRTR
FKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9524.t55 | Gene3D | G3DSA:3.30.160.770 | - | 56 | 161 | 5.5E-56 |
| 7 | g9524.t55 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 55 | - |
| 2 | g9524.t55 | PANTHER | PTHR13718:SF99 | GENE 8225-RELATED | 17 | 178 | 1.2E-76 |
| 3 | g9524.t55 | PANTHER | PTHR13718 | RIBOSOMAL S SUBUNIT | 17 | 178 | 1.2E-76 |
| 1 | g9524.t55 | Pfam | PF00333 | Ribosomal protein S5, N-terminal domain | 99 | 163 | 2.4E-29 |
| 6 | g9524.t55 | ProSitePatterns | PS00585 | Ribosomal protein S5 signature. | 116 | 148 | - |
| 8 | g9524.t55 | ProSiteProfiles | PS50881 | S5 double stranded RNA-binding domain profile. | 99 | 162 | 22.324 |
| 4 | g9524.t55 | SUPERFAMILY | SSF54768 | dsRNA-binding domain-like | 93 | 164 | 1.15E-21 |
| 9 | g9524.t55 | TIGRFAM | TIGR01020 | uS5_euk_arch: ribosomal protein uS5 | 53 | 178 | 4.6E-56 |
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:0003723 | RNA binding | MF |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
| GO:0015935 | small ribosomal subunit | CC |
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.
