General information for g9715.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 40S ribosomal protein S20.
Parent gene
- The parent gene g9715 is located on chr_1: 4777665..4783092 (+ 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 | g9715 | g9715.t12 | TSS | g9715.t12 | 4777068 | 4777068 |
| chr_1 | g9715 | g9715.t12 | isoform | g9715.t12 | 4777159 | 4778147 |
| chr_1 | g9715 | g9715.t12 | exon | g9715.t12.exon1 | 4777159 | 4777161 |
| chr_1 | g9715 | g9715.t12 | cds | g9715.t12.CDS1 | 4777159 | 4777161 |
| chr_1 | g9715 | g9715.t12 | exon | g9715.t12.exon2 | 4777312 | 4777467 |
| chr_1 | g9715 | g9715.t12 | cds | g9715.t12.CDS2 | 4777312 | 4777467 |
| chr_1 | g9715 | g9715.t12 | exon | g9715.t12.exon3 | 4777688 | 4777777 |
| chr_1 | g9715 | g9715.t12 | cds | g9715.t12.CDS3 | 4777688 | 4777777 |
| chr_1 | g9715 | g9715.t12 | exon | g9715.t12.exon4 | 4778046 | 4778147 |
| chr_1 | g9715 | g9715.t12 | cds | g9715.t12.CDS4 | 4778046 | 4778147 |
| chr_1 | g9715 | g9715.t12 | TTS | g9715.t12 | 4778213 | 4778213 |
Sequences
>g9715.t12 Gene=g9715 Length=351
ATGGCGGCCGTTGGTAAAGATATTGAAAAGCAGCAACAAGCTGAAACATCATCAGTTCAT
CGCATTCGCATTGTATTGACTGCATGCAATGTTCGTTCATTGGAAAAAGTTTGCACTGAC
TTGATCTCTGGCGCAAAGAAACAAAAGTTGCGCGTTAAGGGACCAATTCGTATGCCAACA
AATACATTGCGCATCACAACACGTAAAACACCTTGCGGTGAAGGTTCAAAAACCTGGGAT
CGCTTCCAACGTATCATTGATTTGCACTCACCATCAGAAATTGTGCGTCAAATCACATCA
ATTAACATCGAACCAGGTGTACAAGTTGAAGTTACCATTGCCGACAATTAA
>g9715.t12 Gene=g9715 Length=116
MAAVGKDIEKQQQAETSSVHRIRIVLTACNVRSLEKVCTDLISGAKKQKLRVKGPIRMPT
NTLRITTRKTPCGEGSKTWDRFQRIIDLHSPSEIVRQITSINIEPGVQVEVTIADN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9715.t12 | Gene3D | G3DSA:3.30.70.600 | - | 6 | 115 | 0.00000 |
| 4 | g9715.t12 | Hamap | MF_00508 | 30S ribosomal protein S10 [rpsJ]. | 19 | 113 | 13.91788 |
| 2 | g9715.t12 | PANTHER | PTHR11700 | 30S RIBOSOMAL PROTEIN S10 FAMILY MEMBER | 9 | 115 | 0.00000 |
| 3 | g9715.t12 | PANTHER | PTHR11700:SF8 | 40S RIBOSOMAL PROTEIN S20 | 9 | 115 | 0.00000 |
| 1 | g9715.t12 | Pfam | PF00338 | Ribosomal protein S10p/S20e | 23 | 112 | 0.00000 |
| 6 | g9715.t12 | SMART | SM01403 | Ribosomal_S10_2 | 23 | 112 | 0.00000 |
| 5 | g9715.t12 | SUPERFAMILY | SSF54999 | Ribosomal protein S10 | 21 | 113 | 0.00000 |
| 8 | g9715.t12 | TIGRFAM | TIGR01046 | uS10_euk_arch: ribosomal protein uS10 | 20 | 113 | 0.00000 |
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: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. There were no conditions that were differentially expressed