General information for g11017.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L18.
Parent gene
- The parent gene g11017 is located on chr_1: 13420889..13429757 (- 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 | g11017 | g11017.t20 | TTS | g11017.t20 | 13420777 | 13420777 |
| chr_1 | g11017 | g11017.t20 | isoform | g11017.t20 | 13420889 | 13421756 |
| chr_1 | g11017 | g11017.t20 | exon | g11017.t20.exon1 | 13420889 | 13421368 |
| chr_1 | g11017 | g11017.t20 | cds | g11017.t20.CDS1 | 13420889 | 13421368 |
| chr_1 | g11017 | g11017.t20 | exon | g11017.t20.exon2 | 13421566 | 13421628 |
| chr_1 | g11017 | g11017.t20 | cds | g11017.t20.CDS2 | 13421566 | 13421628 |
| chr_1 | g11017 | g11017.t20 | exon | g11017.t20.exon3 | 13421754 | 13421756 |
| chr_1 | g11017 | g11017.t20 | cds | g11017.t20.CDS3 | 13421754 | 13421756 |
| chr_1 | g11017 | g11017.t20 | TSS | g11017.t20 | 13421778 | 13421778 |
Sequences
>g11017.t20 Gene=g11017 Length=546
ATGGGCAAGGACATTAGTCATAAGTGGGACAGAAAAGTCCGCAGAACATCTCCAAAATCA
TTGGATCTTTATCGCTTCCTGTATCGCAGAACTCATCAGAAGTTCAATAAAATCATTCTG
CGACGTTTATTCATGAGTAAAATCAACCGCCCAGTGATTTCGTTGCAACGCGTAATCCGT
TTGATGAAACAACGTCAAGCAAAGGAAAACACAATTGCAGTTATTGTTGGCAAAGTTACA
AATGACTTGAGAATTTTGGAAGTACCAAAATTGCGCATCTGTGCATTAAGAGTTAGTGAA
CGTGCCCGTGAGCGCATTATTAAGAGTGGCGGTGAAGTTTTAACTTTCGATCAATTGGCA
TTGCTCGCACCTACTGGCAAAAACACAATCTTGATGCAAGGTAAACGCAATAATCGTGAG
GCCGTAACACACTTTGGAAAAGCTCCTGGTGTACCTCATTCCCATACAAGACCATACGTT
CGATCAAAAGGACGTAAATTCGAACGCGCTCGTGGTCGCAGAACATCATGCGGATACAAG
AAGTAA
>g11017.t20 Gene=g11017 Length=181
MGKDISHKWDRKVRRTSPKSLDLYRFLYRRTHQKFNKIILRRLFMSKINRPVISLQRVIR
LMKQRQAKENTIAVIVGKVTNDLRILEVPKLRICALRVSERARERIIKSGGEVLTFDQLA
LLAPTGKNTILMQGKRNNREAVTHFGKAPGVPHSHTRPYVRSKGRKFERARGRRTSCGYK
K
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11017.t20 | Gene3D | G3DSA:3.100.10.10 | - | 1 | 181 | 7.3E-83 |
| 2 | g11017.t20 | PANTHER | PTHR10934 | 60S RIBOSOMAL PROTEIN L18 | 1 | 180 | 1.2E-73 |
| 3 | g11017.t20 | PANTHER | PTHR10934:SF2 | 60S RIBOSOMAL PROTEIN L18 | 1 | 180 | 1.2E-73 |
| 1 | g11017.t20 | Pfam | PF17135 | Ribosomal protein 60S L18 and 50S L18e | 3 | 181 | 4.6E-80 |
| 5 | g11017.t20 | ProSitePatterns | PS01106 | Ribosomal protein L18e signature. | 41 | 58 | - |
| 4 | g11017.t20 | SUPERFAMILY | SSF52080 | Ribosomal proteins L15p and L18e | 20 | 133 | 3.05E-24 |
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 K02883 (large subunit ribosomal protein L18e)
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.
