General information for g9265.t60
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L15.
Parent gene
- The parent gene g9265 is located on chr_1: 1368748..1372354 (- 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 | g9265 | g9265.t60 | TTS | g9265.t60 | 1368157 | 1368157 |
| chr_1 | g9265 | g9265.t60 | isoform | g9265.t60 | 1368266 | 1369054 |
| chr_1 | g9265 | g9265.t60 | exon | g9265.t60.exon1 | 1368266 | 1368571 |
| chr_1 | g9265 | g9265.t60 | cds | g9265.t60.CDS1 | 1368266 | 1368571 |
| chr_1 | g9265 | g9265.t60 | exon | g9265.t60.exon2 | 1368749 | 1369054 |
| chr_1 | g9265 | g9265.t60 | cds | g9265.t60.CDS2 | 1368749 | 1369054 |
| chr_1 | g9265 | g9265.t60 | TSS | g9265.t60 | 1369484 | 1369484 |
Sequences
>g9265.t60 Gene=g9265 Length=612
GGTGCGTACAGATACGTTCAAGAGTTATATCGCAAAAAGCAGAGCGATGTTCTTCGCTAT
TTGCTTCGAGTTAGATGCTGGCAATATCGTCAATTGACTAAATTGCATCGTGCTCCACGT
CCATCACGTCCTGATAAAGCACGTCGTCTTGGTTATCGTGCAAAGCAAGGATTTTTGATC
TATCGCATTCGTGTTCGCCGTGGAGGTCGCAAACGTCCAGTACACAAGGGATGCACATAT
GGCAAACCAAAAAGTCATGGTGTTAACCAATTGAAGCCATACAGAAATTTGCAATCTGTT
GCTGAGGAACGTGTTGGTCGACGATTGGGAGGACTTCGTGTTCTCAATTCATACTGGGTC
GCACAAGATGCTGCATTCAAATATTACGAAGTCATCTGCATCGATCCATTCCACAATGCT
ATTCGTCGTGATCCTAAAGTTAACTGGATTTGTAATGCTGTTCACAAGCATCGTGAATTA
CGCGGACTTACATCTGCCGGAAAGAGCTCACGCGGTATTGGAAAAGGATACAGATATTCA
CAAACTATTGGTGGCTCACGTCGTGCTGCATGGCGTCGAAAGAATCGCCTCCATCTCCGT
CGCTATCGTTAA
>g9265.t60 Gene=g9265 Length=203
GAYRYVQELYRKKQSDVLRYLLRVRCWQYRQLTKLHRAPRPSRPDKARRLGYRAKQGFLI
YRIRVRRGGRKRPVHKGCTYGKPKSHGVNQLKPYRNLQSVAEERVGRRLGGLRVLNSYWV
AQDAAFKYYEVICIDPFHNAIRRDPKVNWICNAVHKHRELRGLTSAGKSSRGIGKGYRYS
QTIGGSRRAAWRRKNRLHLRRYR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9265.t60 | Gene3D | G3DSA:3.40.1120.10 | Ribosomal protein l15e | 1 | 196 | 4.2E-103 |
| 2 | g9265.t60 | PANTHER | PTHR11847:SF4 | 60S RIBOSOMAL PROTEIN L15 | 1 | 203 | 2.3E-99 |
| 3 | g9265.t60 | PANTHER | PTHR11847 | RIBOSOMAL PROTEIN L15 | 1 | 203 | 2.3E-99 |
| 1 | g9265.t60 | Pfam | PF00827 | Ribosomal L15 | 1 | 189 | 1.4E-88 |
| 6 | g9265.t60 | ProSitePatterns | PS01194 | Ribosomal protein L15e signature. | 45 | 68 | - |
| 5 | g9265.t60 | SMART | SM01384 | Ribosomal_L15e_2 | 1 | 192 | 2.5E-133 |
| 4 | g9265.t60 | SUPERFAMILY | SSF54189 | Ribosomal proteins S24e, L23 and L15e | 1 | 193 | 4.7E-89 |
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 K02877 (large subunit ribosomal protein L15e)
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.
