General information for g2608.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 40S ribosomal protein S12.
Parent gene
- The parent gene g2608 is located on chr_3: 19031732..19032353 (+ 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 | g2608 | g2608.t1 | TSS | g2608.t1 | 19031543 | 19031543 |
| chr_3 | g2608 | g2608.t1 | isoform | g2608.t1 | 19031621 | 19032276 |
| chr_3 | g2608 | g2608.t1 | exon | g2608.t1.exon1 | 19031621 | 19031634 |
| chr_3 | g2608 | g2608.t1 | cds | g2608.t1.CDS1 | 19031621 | 19031634 |
| chr_3 | g2608 | g2608.t1 | exon | g2608.t1.exon2 | 19031732 | 19031869 |
| chr_3 | g2608 | g2608.t1 | cds | g2608.t1.CDS2 | 19031732 | 19031869 |
| chr_3 | g2608 | g2608.t1 | exon | g2608.t1.exon3 | 19032009 | 19032276 |
| chr_3 | g2608 | g2608.t1 | cds | g2608.t1.CDS3 | 19032009 | 19032276 |
| chr_3 | g2608 | g2608.t1 | TTS | g2608.t1 | 19032355 | 19032355 |
Sequences
>g2608.t1 Gene=g2608 Length=420
ATGTCAGATACTGAAGAAGCCGCAGCTCCAGTTGCTGTCTCATTGGATGGCGCTATGGAC
TTAAATACTGCTCTTCAGGAAGTTTTGAAGCAATCACTTGTTAGTGATGGTTTAGTTCAT
GGAATTCATCAGGCATGCAAAGTTTTGGACAAACGCCAAGCCGTATTGTGTATTCTCTCT
GAGAGCTGTGATGAGCCTCAATACAAACAACTCATTACTGCTTTGTGCAACGAGCATCAA
ATCCCATTGATTCGTGTCGATAGCAGCAAAAAATTAGGTGAATGGTCAGGTCTTTGCAAG
ATCGACAAAGAGGGCAAACCAAGAAAGATTTGCGGATGTTCCTGTGTCGTTATTAAAAAC
TTTGGTCAAGAAACACCAGCTTTGGACATTGTCAAGCAGCACTTGCGTTCATCAGCTTAA
>g2608.t1 Gene=g2608 Length=139
MSDTEEAAAPVAVSLDGAMDLNTALQEVLKQSLVSDGLVHGIHQACKVLDKRQAVLCILS
ESCDEPQYKQLITALCNEHQIPLIRVDSSKKLGEWSGLCKIDKEGKPRKICGCSCVVIKN
FGQETPALDIVKQHLRSSA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g2608.t1 | Gene3D | G3DSA:3.30.1330.30 | - | 1 | 138 | 2.4E-59 |
| 2 | g2608.t1 | PANTHER | PTHR11843 | 40S RIBOSOMAL PROTEIN S12 | 6 | 137 | 4.1E-52 |
| 3 | g2608.t1 | PANTHER | PTHR11843:SF0 | 40S RIBOSOMAL PROTEIN S12 | 6 | 137 | 4.1E-52 |
| 6 | g2608.t1 | PRINTS | PR00972 | Ribosomal protein S12E family signature | 28 | 41 | 1.9E-27 |
| 5 | g2608.t1 | PRINTS | PR00972 | Ribosomal protein S12E family signature | 42 | 58 | 1.9E-27 |
| 4 | g2608.t1 | PRINTS | PR00972 | Ribosomal protein S12E family signature | 83 | 104 | 1.9E-27 |
| 7 | g2608.t1 | PRINTS | PR00972 | Ribosomal protein S12E family signature | 108 | 121 | 1.9E-27 |
| 1 | g2608.t1 | Pfam | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | 24 | 117 | 7.4E-27 |
| 9 | g2608.t1 | ProSitePatterns | PS01189 | Ribosomal protein S12e signature. | 24 | 42 | - |
| 8 | g2608.t1 | SUPERFAMILY | SSF55315 | L30e-like | 14 | 135 | 6.48E-31 |
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 K02951 (small subunit ribosomal protein S12e)
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.
