General information for g11600.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S3.
Parent gene
- The parent gene g11600 is located on chr_1: 17409067..17410315 (- 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 | g11600 | g11600.t1 | TTS | g11600.t1 | 17408974 | 17408974 |
| chr_1 | g11600 | g11600.t1 | isoform | g11600.t1 | 17409067 | 17410315 |
| chr_1 | g11600 | g11600.t1 | exon | g11600.t1.exon1 | 17409067 | 17409574 |
| chr_1 | g11600 | g11600.t1 | cds | g11600.t1.CDS1 | 17409067 | 17409574 |
| chr_1 | g11600 | g11600.t1 | exon | g11600.t1.exon2 | 17409631 | 17409827 |
| chr_1 | g11600 | g11600.t1 | cds | g11600.t1.CDS2 | 17409631 | 17409827 |
| chr_1 | g11600 | g11600.t1 | exon | g11600.t1.exon3 | 17410286 | 17410315 |
| chr_1 | g11600 | g11600.t1 | cds | g11600.t1.CDS3 | 17410286 | 17410315 |
| chr_1 | g11600 | g11600.t1 | TSS | g11600.t1 | 17410361 | 17410361 |
Sequences
>g11600.t1 Gene=g11600 Length=735
ATGAACACTGCAATTTCAAAAAAACGCAAGTTTGTCGCCGCTGGCGTCTTTAAAGCTGAA
TTGAATGAGTTTTTAACTCGAGAGCTCGCAGAGGATGGATATTCAGGAGTTGAAGTACGT
GTGACACCATCAAGAACAGAAATCATTATTATGGCCACAAGAACTCAAAATGTTTTGGGT
GAAAAAGGTCGTCGTATTCGTGAATTAACAGCTGTTGTACAAAAGAGATTCAATTTTGCA
CCCGGTGCAGTTGAATTGTATGCTGAAAAAGTTGCTACCCGTGGTCTCTGCGCTATTGCA
CAAGCCGAGTCTCTTCGATACAAACTCATTGGTGGCTTAGCTGTTCGTCGTGCATGCTAT
GGTGTTCTTCGCTTCATTATGGAATCAGGAGCTAAGGGCTGCGAAGTTGTTGTATCTGGC
AAACTTAGAGGTCAACGTGCCAAGTCAATGAAATTTGTTGATGGGTTGATGATTCATTCA
GGTGATCCTTGCAATGACTACGTTGATACAGCCACACGTCATGTCTTATTGAGACAAGGA
GTATTGGGAATTAAGGTCAAAATTATGCTACCATGGGATCCATCAGGCAAAATTGGTCCA
AAACGACCATTGCCAGATAACGTTTCGGTTGTTGAACCTAAAGATGAGATCGTATATTTG
AAACCTGACACCGAATACAAAGGCAAACCAGCATATATTGGTGCTGAAGAACAGCAGCAT
GTCGAAGCTAAGTAA
>g11600.t1 Gene=g11600 Length=244
MNTAISKKRKFVAAGVFKAELNEFLTRELAEDGYSGVEVRVTPSRTEIIIMATRTQNVLG
EKGRRIRELTAVVQKRFNFAPGAVELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTATRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKRPLPDNVSVVEPKDEIVYLKPDTEYKGKPAYIGAEEQQH
VEAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11600.t1 | CDD | cd02413 | 40S_S3_KH | 15 | 95 | 3.98727E-51 |
| 7 | g11600.t1 | Gene3D | G3DSA:3.30.300.20 | - | 1 | 91 | 1.4E-46 |
| 8 | g11600.t1 | Gene3D | G3DSA:3.30.1140.32 | - | 93 | 220 | 1.9E-70 |
| 3 | g11600.t1 | PANTHER | PTHR11760:SF36 | 40S RIBOSOMAL PROTEIN S3 | 1 | 233 | 1.2E-137 |
| 4 | g11600.t1 | PANTHER | PTHR11760 | 30S/40S RIBOSOMAL PROTEIN S3 | 1 | 233 | 1.2E-137 |
| 1 | g11600.t1 | Pfam | PF07650 | KH domain | 20 | 93 | 2.9E-11 |
| 2 | g11600.t1 | Pfam | PF00189 | Ribosomal protein S3, C-terminal domain | 106 | 188 | 6.2E-23 |
| 10 | g11600.t1 | ProSitePatterns | PS00548 | Ribosomal protein S3 signature. | 147 | 183 | - |
| 11 | g11600.t1 | ProSiteProfiles | PS50823 | Type-2 KH domain profile. | 21 | 92 | 11.916 |
| 5 | g11600.t1 | SUPERFAMILY | SSF54814 | Prokaryotic type KH domain (KH-domain type II) | 10 | 99 | 5.76E-25 |
| 6 | g11600.t1 | SUPERFAMILY | SSF54821 | Ribosomal protein S3 C-terminal domain | 94 | 192 | 4.71E-28 |
| 12 | g11600.t1 | TIGRFAM | TIGR01008 | uS3_euk_arch: ribosomal protein uS3 | 8 | 211 | 3.2E-72 |
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 |
KEGG
Orthology
- This transcript has been annotated with K02985 (small subunit ribosomal protein S3e)
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.
