General information for g9278.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S10b.
Parent gene
- The parent gene g9278 is located on chr_1: 1399153..1400944 (+ 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 | g9278 | g9278.t20 | TSS | g9278.t20 | 1399145 | 1399145 |
| chr_1 | g9278 | g9278.t20 | isoform | g9278.t20 | 1399146 | 1399725 |
| chr_1 | g9278 | g9278.t20 | exon | g9278.t20.exon1 | 1399146 | 1399345 |
| chr_1 | g9278 | g9278.t20 | cds | g9278.t20.CDS1 | 1399146 | 1399345 |
| chr_1 | g9278 | g9278.t20 | exon | g9278.t20.exon2 | 1399400 | 1399611 |
| chr_1 | g9278 | g9278.t20 | cds | g9278.t20.CDS2 | 1399400 | 1399611 |
| chr_1 | g9278 | g9278.t20 | exon | g9278.t20.exon3 | 1399687 | 1399725 |
| chr_1 | g9278 | g9278.t20 | cds | g9278.t20.CDS3 | 1399687 | 1399724 |
| chr_1 | g9278 | g9278.t20 | TTS | g9278.t20 | 1399800 | 1399800 |
Sequences
>g9278.t20 Gene=g9278 Length=451
ATGTTTATGCCAAAAGCACATAAAGTGGCGATCTATGAACATCTCTTCAAAGAAGGAGTT
CTTGTTGCACAAAAGGATTTTCATGCACCAAAACATCCCGAACTCGAGAGCGTTCCAAAT
CTTCATGTAATTAAGACTATGCAGTCATTGAAATCAAGAAATCTTGTTAAGGAACAATTT
GCATGGAGACATTATTACTGGTATCTCACAAATGAAGGCATTGAATATTTGCGTCAATAT
CTTCATTTGCCACCAGAAATCGTTCCATCAACATTGAAGCGAACAACTCGCTCAGATGCT
GCTCGTCCTCGCGCTGCTCCACGTTCAGATGGACCAAAATCAGGAGAAGATCGTCAAGCA
TACAGACGTGCACCAGGGCAATCGTCAGACAAAAAAGCCGATGTTGGTGCTGCGTGGTGG
ATTCGGTCGTGGCTCAAGAGGCCCACAGTAA
>g9278.t20 Gene=g9278 Length=150
MFMPKAHKVAIYEHLFKEGVLVAQKDFHAPKHPELESVPNLHVIKTMQSLKSRNLVKEQF
AWRHYYWYLTNEGIEYLRQYLHLPPEIVPSTLKRTTRSDAARPRAAPRSDGPKSGEDRQA
YRRAPGQSSDKKADVGAAWWIRSWLKRPTV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9278.t20 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 1 | 107 | 2.9E-50 |
| 4 | g9278.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 92 | 134 | - |
| 3 | g9278.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 97 | 129 | - |
| 2 | g9278.t20 | PANTHER | PTHR12146 | 40S RIBOSOMAL PROTEIN S10 | 1 | 137 | 1.9E-57 |
| 1 | g9278.t20 | Pfam | PF03501 | Plectin/S10 domain | 3 | 95 | 2.5E-46 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K02947 (small subunit ribosomal protein S10e)
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