General information for g9265.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t28 | isoform | g9265.t28 | 1368153 | 1369239 |
| chr_1 | g9265 | g9265.t28 | exon | g9265.t28.exon1 | 1368153 | 1369078 |
| chr_1 | g9265 | g9265.t28 | TTS | g9265.t28 | 1368157 | 1368157 |
| chr_1 | g9265 | g9265.t28 | cds | g9265.t28.CDS1 | 1368734 | 1369057 |
| chr_1 | g9265 | g9265.t28 | exon | g9265.t28.exon2 | 1369217 | 1369239 |
| chr_1 | g9265 | g9265.t28 | TSS | g9265.t28 | 1369484 | 1369484 |
Sequences
>g9265.t28 Gene=g9265 Length=949
AGATAGACGATTTATAAATACAGGTCTATCATTAATCGTAAATAATGGGTGCGTACAGAT
ACGTTCAAGAGTTATATCGCAAAAAGCAGAGCGATGTTCTTCGCTATTTGCTTCGAGTTA
GATGCTGGCAATATCGTCAATTGACTAAATTGCATCGTGCTCCACGTCCATCACGTCCTG
ATAAAGCACGTCGTCTTGGTTATCGTGCAAAGCAAGGATTTTTGATCTATCGCATTCGTG
TTCGCCGTGGAGGTCGCAAACGTCCAGTACACAAGGGATGCACATATGGCAAACCAAAAA
GTCATGGTGTTAACCAATTGAAGCCATACAGAAATTTGCAATCTGTTGCTGAGGTAAATA
TCCTATGAAATCTACTGTAATATTATTAGTTTTGAATGATGATAGCATTTCAAATTCACA
CTGAATATAATTTGATGTGCTTTTAACTTCCTTAGATGTCTGAATTAGTTTCTTAAATAT
GCTATCAATATATTTTTCAATAGAAATGTATTAATGTACATATTTTTTAGGAACGTGTTG
GTCGACGATTGGGAGGACTTCGTGTTCTCAATTCATACTGGGTCGCACAAGATGCTGCAT
TCAAATATTACGAAGTCATCTGCATCGATCCATTCCACAATGCTATTCGTCGTGATCCTA
AAGTTAACTGGATTTGTAATGCTGTTCACAAGCATCGTGAATTACGCGGACTTACATCTG
CCGGAAAGAGCTCACGCGGTATTGGAAAAGGATACAGATATTCACAAACTATTGGTGGCT
CACGTCGTGCTGCATGGCGTCGAAAGAATCGCCTCCATCTCCGTCGCTATCGTTAAAATG
GAAATACACATTAAATCGATTTATTTTGTGTATATTGTTATAAACATCTTAACAATTTTT
TTCAAAAATGAATAAATTTCATATATCAAAAACAATATGAAACTCAAAA
>g9265.t28 Gene=g9265 Length=107
MGAYRYVQELYRKKQSDVLRYLLRVRCWQYRQLTKLHRAPRPSRPDKARRLGYRAKQGFL
IYRIRVRRGGRKRPVHKGCTYGKPKSHGVNQLKPYRNLQSVAEVNIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9265.t28 | Gene3D | G3DSA:3.40.1120.10 | Ribosomal protein l15e | 1 | 106 | 6.5E-53 |
| 2 | g9265.t28 | PANTHER | PTHR11847:SF4 | 60S RIBOSOMAL PROTEIN L15 | 1 | 104 | 7.4E-50 |
| 3 | g9265.t28 | PANTHER | PTHR11847 | RIBOSOMAL PROTEIN L15 | 1 | 104 | 7.4E-50 |
| 1 | g9265.t28 | Pfam | PF00827 | Ribosomal L15 | 2 | 104 | 5.7E-42 |
| 6 | g9265.t28 | ProSitePatterns | PS01194 | Ribosomal protein L15e signature. | 46 | 69 | - |
| 5 | g9265.t28 | SMART | SM01384 | Ribosomal_L15e_2 | 2 | 107 | 3.0E-31 |
| 4 | g9265.t28 | SUPERFAMILY | SSF54189 | Ribosomal proteins S24e, L23 and L15e | 1 | 103 | 4.65E-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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
