General information for g9066.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 40S ribosomal protein S23.
Parent gene
- The parent gene g9066 is located on chr_2: 35014380..35022094 (- 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 | g9066 | g9066.t28 | TTS | g9066.t28 | 35013961 | 35013961 |
| chr_2 | g9066 | g9066.t28 | isoform | g9066.t28 | 35014027 | 35015255 |
| chr_2 | g9066 | g9066.t28 | exon | g9066.t28.exon1 | 35014027 | 35014133 |
| chr_2 | g9066 | g9066.t28 | cds | g9066.t28.CDS1 | 35014083 | 35014133 |
| chr_2 | g9066 | g9066.t28 | exon | g9066.t28.exon2 | 35014342 | 35014474 |
| chr_2 | g9066 | g9066.t28 | cds | g9066.t28.CDS2 | 35014342 | 35014474 |
| chr_2 | g9066 | g9066.t28 | exon | g9066.t28.exon3 | 35014697 | 35014854 |
| chr_2 | g9066 | g9066.t28 | cds | g9066.t28.CDS3 | 35014697 | 35014722 |
| chr_2 | g9066 | g9066.t28 | exon | g9066.t28.exon4 | 35015252 | 35015255 |
| chr_2 | g9066 | g9066.t28 | TSS | g9066.t28 | 35015280 | 35015280 |
Sequences
>g9066.t28 Gene=g9066 Length=402
ATGGGAAAACCAAGAGGAATTCGAACTGCTCGTAAGCTTAAAACACACAGACGTGACCAA
CGATGGGCTGACAAAGATTATAAGAAAGCTCACTTGGGTACTCGCTGGAAGGCAAATCCA
TTTGGAGGTGCATCTCATGCTAAGGGAATCGTTCTTGAAAAATGGTGTTGAAGCTAAACA
GCCAAACTCAGCTATCCGCAAGTGCGTTCGTGTACAATTGATCAAGAATGGCAAGAAAAT
TACCGCTTTCGTTCCTCGTGATGGTTGCTTAAACTATATTGAAGAAAATGACGAAAATTT
AACTAACGAATTTCATTTTTATTATCATTTTAGGTCGTCAAAGTAGCAAATGTTTCGCTA
TTGGCCTTATACAAGGAAAAGAAAGAGCGACCACGTTCATAA
>g9066.t28 Gene=g9066 Length=69
MLRESFLKNGVEAKQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDENLTNEFH
FYYHFRSSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9066.t28 | Gene3D | G3DSA:2.40.50.140 | - | 3 | 67 | 5.9E-26 |
| 2 | g9066.t28 | PANTHER | PTHR11652:SF40 | 40S RIBOSOMAL PROTEIN S23-1-RELATED | 8 | 59 | 8.4E-26 |
| 3 | g9066.t28 | PANTHER | PTHR11652 | 30S RIBOSOMAL PROTEIN S12 FAMILY MEMBER | 8 | 59 | 8.4E-26 |
| 1 | g9066.t28 | Pfam | PF00164 | Ribosomal protein S12/S23 | 8 | 55 | 9.4E-22 |
| 5 | g9066.t28 | ProSitePatterns | PS00055 | Ribosomal protein S12 signature. | 14 | 21 | - |
| 4 | g9066.t28 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 9 | 58 | 5.23E-14 |
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 |
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.
