General information for g2823.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 28S ribosomal protein S18c, mitochondrial.
Parent gene
- The parent gene g2823 is located on chr_3: 20441954..20443685 (+ 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_3 | g2823 | g2823.t1 | isoform | g2823.t1 | 20441029 | 20441954 |
| chr_3 | g2823 | g2823.t1 | exon | g2823.t1.exon1 | 20441029 | 20441065 |
| chr_3 | g2823 | g2823.t1 | cds | g2823.t1.CDS1 | 20441029 | 20441065 |
| chr_3 | g2823 | g2823.t1 | exon | g2823.t1.exon2 | 20441136 | 20441472 |
| chr_3 | g2823 | g2823.t1 | cds | g2823.t1.CDS2 | 20441136 | 20441472 |
| chr_3 | g2823 | g2823.t1 | exon | g2823.t1.exon3 | 20441894 | 20441954 |
| chr_3 | g2823 | g2823.t1 | cds | g2823.t1.CDS3 | 20441894 | 20441954 |
| chr_3 | g2823 | g2823.t1 | TTS | g2823.t1 | 20442029 | 20442029 |
| chr_3 | g2823 | g2823.t1 | TSS | g2823.t1 | NA | NA |
Sequences
>g2823.t1 Gene=g2823 Length=435
ATGTTTTTAAAATTAATTCCACAAATTAGCAATGCATTGAAAGGGATCAAAAAACCGCAA
ATGCAGATAAGTGCAAATTTTTGCTCACAAGTATCAAATTTAAATGACTTTAAGAATGAA
GGCGATAGTGATGAACCAATTGAAATGAAGAATCCATTTGAAAAAGAGAAAGTGAAATGT
ATTTTATGCAGAAATAATATCGAACCATCATATAAAAATGTTCAGTTATTGTCTCAATTT
CAATCTCCTTACACTGGTCGAACTTATGGCAGACATATTACAGGATTGTGTAAAAATATG
CAAGAAAAGGTGGAAATGTCAATCATGAGAGCACAACATTTAGGATTTATGGGATATGTT
ACGAAACAACCAAGGTTTCTAAAAGACCCTAAGCTTTTTAATCCGGAAAAACCTCAGAGA
CCTCACAAATATTGA
>g2823.t1 Gene=g2823 Length=144
MFLKLIPQISNALKGIKKPQMQISANFCSQVSNLNDFKNEGDSDEPIEMKNPFEKEKVKC
ILCRNNIEPSYKNVQLLSQFQSPYTGRTYGRHITGLCKNMQEKVEMSIMRAQHLGFMGYV
TKQPRFLKDPKLFNPEKPQRPHKY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2823.t1 | Gene3D | G3DSA:4.10.640.10 | 30s Ribosomal Protein S18 | 36 | 125 | 0 |
| 2 | g2823.t1 | PANTHER | PTHR13479 | 30S RIBOSOMAL PROTEIN S18 | 44 | 134 | 0 |
| 3 | g2823.t1 | PANTHER | PTHR13479:SF57 | 28S RIBOSOMAL PROTEIN S18C, MITOCHONDRIAL | 44 | 134 | 0 |
| 1 | g2823.t1 | Pfam | PF01084 | Ribosomal protein S18 | 66 | 117 | 0 |
| 4 | g2823.t1 | SUPERFAMILY | SSF46911 | Ribosomal protein S18 | 52 | 125 | 0 |
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 transcript has been annotated with K02963 (small subunit ribosomal protein S18)
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.
