General information for g11240.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S acidic ribosomal protein P2.
Parent gene
- The parent gene g11240 is located on chr_1: 14864769..14868315 (- 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 | g11240 | g11240.t23 | TTS | g11240.t23 | 14863763 | 14863763 |
| chr_1 | g11240 | g11240.t23 | isoform | g11240.t23 | 14863777 | 14864903 |
| chr_1 | g11240 | g11240.t23 | exon | g11240.t23.exon1 | 14863777 | 14863878 |
| chr_1 | g11240 | g11240.t23 | cds | g11240.t23.CDS1 | 14863777 | 14863878 |
| chr_1 | g11240 | g11240.t23 | exon | g11240.t23.exon2 | 14864058 | 14864147 |
| chr_1 | g11240 | g11240.t23 | cds | g11240.t23.CDS2 | 14864058 | 14864147 |
| chr_1 | g11240 | g11240.t23 | exon | g11240.t23.exon3 | 14864211 | 14864459 |
| chr_1 | g11240 | g11240.t23 | cds | g11240.t23.CDS3 | 14864211 | 14864459 |
| chr_1 | g11240 | g11240.t23 | exon | g11240.t23.exon4 | 14864625 | 14864903 |
| chr_1 | g11240 | g11240.t23 | TSS | g11240.t23 | NA | NA |
Sequences
>g11240.t23 Gene=g11240 Length=720
ATGGACTCATCATGGTTCAGTTATTTTTTTACACACTAAATTTCATTTCTACTATTTTAA
TTCCTTCGAATTCAACAAAATATTTTAAAATTTTAAAAATGAAAGAAATATTTCGAAATT
TAATCATTTTTAGGGGGGTCAACAGCAAAAAATTATTTTACAAAAGAAAGCTACGCGCTT
GCATCTTTCTTTCTTTTCTGCGACATAAAGTAGAATACACACGATTTTCTAAAATTTTGG
TAATTGACAACGTTTCGTGTCAAATAAACAGACTTAAAAATGCGTTACGTTAGCGCTTAC
CTCTTGGCAGTTTTGGGTGGAAATGCTTCGCCATCAAGTGCAGATCTCCAAAAGATCTTG
TCATCAGTCGGTATTGAAGTTGATAGCGAACGCCTCAACAAAGTCATTGATGAACTTAAA
GGAAAGAGCGTCGAGGAATTAATTGCTCAAGGACGCGAGAAACTCAGCTCAATGCCAAGT
GGTGGTGGTGCTGCTGCTGCACCAGCTGCCGGTAAATTCTCACTCATTCTGCAGAAGCCA
AGAAAGAAGAAAAGAAGCCAGAACCAGAGTCAGAAGAAGAGGATGATGACATGGGCTTCG
GTCTCTTTGAATAAAATGGTTGAAGCAAAAACGGTGTGTATTAGATATAAACTCCATCTT
ATAAGTACAATCAAACTTTGTAAACAAAAGTTTGTAATAAAAATAATCTATACACAATAA
>g11240.t23 Gene=g11240 Length=146
MRYVSAYLLAVLGGNASPSSADLQKILSSVGIEVDSERLNKVIDELKGKSVEELIAQGRE
KLSSMPSGGGAAAAPAAGKFSLILQKPRKKKRSQNQSQKKRMMTWASVSLNKMVEAKTVC
IRYKLHLISTIKLCKQKFVIKIIYTQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g11240.t23 | CDD | cd05833 | Ribosomal_P2 | 1 | 67 | 1.14671E-40 |
| 5 | g11240.t23 | Gene3D | G3DSA:1.10.10.1410 | - | 1 | 59 | 3.5E-29 |
| 4 | g11240.t23 | Hamap | MF_01478 | 50S ribosomal protein L12 [rpl12]. | 2 | 81 | 12.436646 |
| 2 | g11240.t23 | PANTHER | PTHR21141:SF5 | 60S ACIDIC RIBOSOMAL PROTEIN P2 | 1 | 101 | 2.0E-32 |
| 3 | g11240.t23 | PANTHER | PTHR21141 | 60S ACIDIC RIBOSOMAL PROTEIN FAMILY MEMBER | 1 | 101 | 2.0E-32 |
| 1 | g11240.t23 | Pfam | PF00428 | 60s Acidic ribosomal protein | 17 | 78 | 4.7E-13 |
| 7 | g11240.t23 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 8 | g11240.t23 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 9 | g11240.t23 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 10 | g11240.t23 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 21 | - |
| 6 | g11240.t23 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 146 | - |
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:0002182 | cytoplasmic translational elongation | BP |
| GO:0022625 | cytosolic large ribosomal subunit | CC |
| GO:0006414 | translational elongation | 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.
