General information for g9066.t29
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t29 | TTS | g9066.t29 | 35013961 | 35013961 |
| chr_2 | g9066 | g9066.t29 | isoform | g9066.t29 | 35014027 | 35015255 |
| chr_2 | g9066 | g9066.t29 | exon | g9066.t29.exon1 | 35014027 | 35014095 |
| chr_2 | g9066 | g9066.t29 | cds | g9066.t29.CDS1 | 35014027 | 35014095 |
| chr_2 | g9066 | g9066.t29 | exon | g9066.t29.exon2 | 35014276 | 35014474 |
| chr_2 | g9066 | g9066.t29 | cds | g9066.t29.CDS2 | 35014276 | 35014474 |
| chr_2 | g9066 | g9066.t29 | exon | g9066.t29.exon3 | 35014695 | 35014844 |
| chr_2 | g9066 | g9066.t29 | cds | g9066.t29.CDS3 | 35014695 | 35014844 |
| chr_2 | g9066 | g9066.t29 | exon | g9066.t29.exon4 | 35015252 | 35015255 |
| chr_2 | g9066 | g9066.t29 | cds | g9066.t29.CDS4 | 35015252 | 35015253 |
| chr_2 | g9066 | g9066.t29 | TSS | g9066.t29 | 35015280 | 35015280 |
Sequences
>g9066.t29 Gene=g9066 Length=422
ATGGAGGAATTCGAACTGCTCGTAAGCTTAAAACACACAGACGTGACCAACGATGGGCTG
ACAAAGATTATAAGAAAGCTCACTTGGGTACTCGCTGGAAGGCAAATCCATTTGGAGGTG
CATCTCATGCTAAGGGAATCGTTCTTGAAAAAGTTGGTGTTGAAGCTAAACAGCCAAACT
CAGCTATCCGCAAGTGCGTTCGTGTACAATTGATCAAGAATGGCAAGAAAATTACCGCTT
TCGTTCCTCGTGATGGTTGCTTAAACTATATTGAAGAAAATGACGAAGTTTTGGTTGCAG
GTTTTGGTCGTAAAGGTCACGCTGTTGGTGATATTCCCGGAGTAAGATTTAAGGTCGTCA
AAGTAGCAAATGTTTCGCTATTGGCCTTATACAAGGAAAAGAAAGAGCGACCACGTTCAT
AA
>g9066.t29 Gene=g9066 Length=139
GGIRTARKLKTHRRDQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQPNS
AIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVRFKVVK
VANVSLLALYKEKKERPRS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9066.t29 | CDD | cd03367 | Ribosomal_S23 | 22 | 136 | 4.99838E-81 |
| 5 | g9066.t29 | Gene3D | G3DSA:2.40.50.140 | - | 21 | 139 | 3.4E-69 |
| 2 | g9066.t29 | PANTHER | PTHR11652:SF14 | 40S RIBOSOMAL PROTEIN S23 | 2 | 139 | 7.6E-83 |
| 3 | g9066.t29 | PANTHER | PTHR11652 | 30S RIBOSOMAL PROTEIN S12 FAMILY MEMBER | 2 | 139 | 7.6E-83 |
| 6 | g9066.t29 | PIRSF | PIRSF002133 | RPS12p_RPS12a_RPS23e_RPS12o | 12 | 139 | 2.3E-35 |
| 1 | g9066.t29 | Pfam | PF00164 | Ribosomal protein S12/S23 | 26 | 138 | 4.6E-52 |
| 8 | g9066.t29 | ProSitePatterns | PS00055 | Ribosomal protein S12 signature. | 56 | 63 | - |
| 4 | g9066.t29 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 16 | 137 | 1.54E-36 |
| 9 | g9066.t29 | TIGRFAM | TIGR00982 | uS12_E_A: ribosomal protein uS12 | 3 | 138 | 1.1E-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:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
| GO:0015935 | small ribosomal subunit | CC |
KEGG
Orthology
- This transcript has been annotated with K02973 (small subunit ribosomal protein S23e)
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