General information for g11240.t19
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.t19 | TTS | g11240.t19 | 14863763 | 14863763 |
| chr_1 | g11240 | g11240.t19 | isoform | g11240.t19 | 14863777 | 14864903 |
| chr_1 | g11240 | g11240.t19 | exon | g11240.t19.exon1 | 14863777 | 14863878 |
| chr_1 | g11240 | g11240.t19 | exon | g11240.t19.exon2 | 14864058 | 14864168 |
| chr_1 | g11240 | g11240.t19 | cds | g11240.t19.CDS1 | 14864062 | 14864168 |
| chr_1 | g11240 | g11240.t19 | exon | g11240.t19.exon3 | 14864228 | 14864445 |
| chr_1 | g11240 | g11240.t19 | cds | g11240.t19.CDS2 | 14864228 | 14864445 |
| chr_1 | g11240 | g11240.t19 | exon | g11240.t19.exon4 | 14864621 | 14864903 |
| chr_1 | g11240 | g11240.t19 | cds | g11240.t19.CDS3 | 14864621 | 14864892 |
| chr_1 | g11240 | g11240.t19 | TSS | g11240.t19 | NA | NA |
Sequences
>g11240.t19 Gene=g11240 Length=714
ATGGACTCATCATGGTTCAGTTATTTTTTTACACACTAAATTTCATTTCTACTATTTTAA
TTCCTTCGAATTCAACAAAATATTTTAAAATTTTAAAAATGAAAGAAATATTTCGAAATT
TAATCATTTTTAGGGGGGTCAACAGCAAAAAATTATTTTACAAAAGAAAGCTACGCGCTT
GCATCTTTCTTTCTTTTCTGCGACATAAAGTAGAATACACACGATTTTCTAAAATTTTGG
TAATTGACAACGTTTCGTGTCAAATAAACAGACTTAAAAGTAACGCTTACCTCTTGGCAG
TTTTGGGTGGAAATGCTTCGCCATCAAGTGCAGATCTCCAAAAGATCTTGTCATCAGTCG
GTATTGAAGTTGATAGCGAACGCCTCAACAAAGTCATTGATGAACTTAAAGGAAAGAGCG
TCGAGGAATTAATTGCTCAAGGACGCGAGAAACTCAGCTCAATGCCAAGTGGTGGTGGTG
CTGCTGCTGCACCAGCTGCCGGTGGTGCCGCTCCAGCCGCAGCTGCAGAAGCCAAGAAAG
AAGAAAAGAAGCCAGAACCAGAGTCAGAAGAAGAGGATGATGACATGGGCTTCGGTCTCT
TTGAATAAAATGGTTGAAGCAAAAACGGTGTGTATTAGATATAAACTCCATCTTATAAGT
ACAATCAAACTTTGTAAACAAAAGTTTGTAATAAAAATAATCTATACACAATAA
>g11240.t19 Gene=g11240 Length=198
MVQLFFYTLNFISTILIPSNSTKYFKILKMKEIFRNLIIFRGVNSKKLFYKRKLRACIFL
SFLRHKVEYTRFSKILVIDNVSCQINRLKSNAYLLAVLGGNASPSSADLQKILSSVGIEV
DSERLNKVIDELKGKSVEELIAQGREKLSSMPSGGGAAAAPAAGGAAPAAAAEAKKEEKK
PEPESEEEDDDMGFGLFE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g11240.t19 | CDD | cd05833 | Ribosomal_P2 | 92 | 151 | 7.88787E-35 |
| 7 | g11240.t19 | Gene3D | G3DSA:1.10.10.1410 | - | 90 | 145 | 4.0E-25 |
| 4 | g11240.t19 | Hamap | MF_01478 | 50S ribosomal protein L12 [rpl12]. | 88 | 198 | 16.839512 |
| 6 | g11240.t19 | MobiDBLite | mobidb-lite | consensus disorder prediction | 148 | 198 | - |
| 5 | g11240.t19 | MobiDBLite | mobidb-lite | consensus disorder prediction | 183 | 198 | - |
| 2 | g11240.t19 | PANTHER | PTHR21141:SF5 | 60S ACIDIC RIBOSOMAL PROTEIN P2 | 91 | 198 | 6.1E-40 |
| 3 | g11240.t19 | PANTHER | PTHR21141 | 60S ACIDIC RIBOSOMAL PROTEIN FAMILY MEMBER | 91 | 198 | 6.1E-40 |
| 1 | g11240.t19 | Pfam | PF00428 | 60s Acidic ribosomal protein | 103 | 197 | 8.5E-27 |
| 9 | g11240.t19 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 10 | g11240.t19 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 8 | g11240.t19 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 26 | 198 | - |
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 transcript has been annotated with K02943 (large subunit ribosomal protein LP2)
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