General information for g11289.t1
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.t1 | TTS | g11289.t1 | 15429083 | 15429083 |
| chr_1 | g11289 | g11289.t1 | isoform | g11289.t1 | 15429166 | 15429885 |
| chr_1 | g11289 | g11289.t1 | exon | g11289.t1.exon1 | 15429166 | 15429491 |
| chr_1 | g11289 | g11289.t1 | cds | g11289.t1.CDS1 | 15429166 | 15429491 |
| chr_1 | g11289 | g11289.t1 | exon | g11289.t1.exon2 | 15429554 | 15429637 |
| chr_1 | g11289 | g11289.t1 | cds | g11289.t1.CDS2 | 15429554 | 15429637 |
| chr_1 | g11289 | g11289.t1 | exon | g11289.t1.exon3 | 15429873 | 15429885 |
| chr_1 | g11289 | g11289.t1 | cds | g11289.t1.CDS3 | 15429873 | 15429885 |
| chr_1 | g11289 | g11289.t1 | TSS | g11289.t1 | 15429913 | 15429913 |
Sequences
>g11289.t1 Gene=g11289 Length=423
ATGTCGAAGAGAGGTCGTGGAGGTTCCGCGGGAGGAAAATTCCGTATTTCACTCGGTATG
CCTGTTGGCGCAGTAATTAATTGTGCAGATAATACAGGTGGTAAAAACTTGTATGTTATT
GCTGTTCATGGCATTCGCGGTCGTTTGAATCGTTTACCTTCAGCTGGTGTTGGTGACATG
TTTGTCGCAACTGTAAAGAAGGGTAAACCAGAATTGAGAAAGAAAGTAATGCCAGCAGTT
GTCATTCGGCAGCGAAAACCGTTCAGACGACGAGATGGAATCTTTATCTATTTTGAAGAT
AACGCCGGTGTAATTGTCAACAATAAAGGTGAAATGAAAGGATCAGCTATTACAGGTCCA
GTTGCAAAAGAGTGTGCAGATTTATGGCCCCGTATTGCATCAAATGCTGGCTCAATAGCC
TAA
>g11289.t1 Gene=g11289 Length=140
MSKRGRGGSAGGKFRISLGMPVGAVINCADNTGGKNLYVIAVHGIRGRLNRLPSAGVGDM
FVATVKKGKPELRKKVMPAVVIRQRKPFRRRDGIFIYFEDNAGVIVNNKGEMKGSAITGP
VAKECADLWPRIASNAGSIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11289.t1 | Gene3D | G3DSA:2.40.150.20 | Ribosomal Protein L14; | 1 | 140 | 7.5E-70 |
| 4 | g11289.t1 | Hamap | MF_01367 | 50S ribosomal protein L14 [rplN]. | 19 | 140 | 19.220411 |
| 2 | g11289.t1 | PANTHER | PTHR11761 | 50S/60S RIBOSOMAL PROTEIN L14/L23 | 1 | 140 | 8.2E-83 |
| 3 | g11289.t1 | PANTHER | PTHR11761:SF22 | 60S RIBOSOMAL PROTEIN L23 | 1 | 140 | 8.2E-83 |
| 1 | g11289.t1 | Pfam | PF00238 | Ribosomal protein L14p/L23e | 22 | 138 | 7.2E-35 |
| 7 | g11289.t1 | ProSitePatterns | PS00049 | Ribosomal protein L14 signature. | 79 | 105 | - |
| 6 | g11289.t1 | SMART | SM01374 | Ribosomal_L14_2 | 19 | 140 | 3.8E-58 |
| 5 | g11289.t1 | SUPERFAMILY | SSF50193 | Ribosomal protein L14 | 12 | 138 | 2.22E-46 |
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.
