General information for g11289.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L23.
Parent gene
- The parent gene g11289 is located on chr_1: 15429166..15429885 (- 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 | g11289 | g11289.t3 | TTS | g11289.t3 | 15429083 | 15429083 |
| chr_1 | g11289 | g11289.t3 | isoform | g11289.t3 | 15429166 | 15429638 |
| chr_1 | g11289 | g11289.t3 | exon | g11289.t3.exon1 | 15429166 | 15429491 |
| chr_1 | g11289 | g11289.t3 | cds | g11289.t3.CDS1 | 15429166 | 15429491 |
| chr_1 | g11289 | g11289.t3 | exon | g11289.t3.exon2 | 15429554 | 15429638 |
| chr_1 | g11289 | g11289.t3 | cds | g11289.t3.CDS2 | 15429554 | 15429593 |
| chr_1 | g11289 | g11289.t3 | TSS | g11289.t3 | 15429913 | 15429913 |
Sequences
>g11289.t3 Gene=g11289 Length=411
GGTCGTGGAGGTTCCGCGGGAGGAAAATTCCGTATTTCACTCGGTATGCCTGTTGGCGCA
GTAATTAATTGTGCAGATAATACAGGTGGTAAAAACTTGTATGTTATTGCTGTTCATGGC
ATTCGCGGTCGTTTGAATCGTTTACCTTCAGCTGGTGTTGGTGACATGTTTGTCGCAACT
GTAAAGAAGGGTAAACCAGAATTGAGAAAGAAAGTAATGCCAGCAGTTGTCATTCGGCAG
CGAAAACCGTTCAGACGACGAGATGGAATCTTTATCTATTTTGAAGATAACGCCGGTGTA
ATTGTCAACAATAAAGGTGAAATGAAAGGATCAGCTATTACAGGTCCAGTTGCAAAAGAG
TGTGCAGATTTATGGCCCCGTATTGCATCAAATGCTGGCTCAATAGCCTAA
>g11289.t3 Gene=g11289 Length=121
MPVGAVINCADNTGGKNLYVIAVHGIRGRLNRLPSAGVGDMFVATVKKGKPELRKKVMPA
VVIRQRKPFRRRDGIFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWPRIASNAGSI
A
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11289.t3 | Gene3D | G3DSA:2.40.150.20 | Ribosomal Protein L14; | 1 | 121 | 1.1E-62 |
| 4 | g11289.t3 | Hamap | MF_01367 | 50S ribosomal protein L14 [rplN]. | 1 | 121 | 17.824255 |
| 2 | g11289.t3 | PANTHER | PTHR11761 | 50S/60S RIBOSOMAL PROTEIN L14/L23 | 1 | 121 | 5.1E-71 |
| 3 | g11289.t3 | PANTHER | PTHR11761:SF22 | 60S RIBOSOMAL PROTEIN L23 | 1 | 121 | 5.1E-71 |
| 1 | g11289.t3 | Pfam | PF00238 | Ribosomal protein L14p/L23e | 3 | 119 | 4.2E-35 |
| 7 | g11289.t3 | ProSitePatterns | PS00049 | Ribosomal protein L14 signature. | 60 | 86 | - |
| 6 | g11289.t3 | SMART | SM01374 | Ribosomal_L14_2 | 2 | 121 | 8.4E-57 |
| 5 | g11289.t3 | SUPERFAMILY | SSF50193 | Ribosomal protein L14 | 2 | 119 | 5.1E-45 |
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 K02894 (large subunit ribosomal protein L23e)
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