General information for g9265.t88
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.t88 | TTS | g9265.t88 | 1368157 | 1368157 |
| chr_1 | g9265 | g9265.t88 | isoform | g9265.t88 | 1368266 | 1369667 |
| chr_1 | g9265 | g9265.t88 | exon | g9265.t88.exon1 | 1368266 | 1368571 |
| chr_1 | g9265 | g9265.t88 | cds | g9265.t88.CDS1 | 1368268 | 1368571 |
| chr_1 | g9265 | g9265.t88 | exon | g9265.t88.exon2 | 1368768 | 1369078 |
| chr_1 | g9265 | g9265.t88 | cds | g9265.t88.CDS2 | 1368768 | 1369057 |
| chr_1 | g9265 | g9265.t88 | exon | g9265.t88.exon3 | 1369435 | 1369667 |
| chr_1 | g9265 | g9265.t88 | TSS | g9265.t88 | NA | NA |
Sequences
>g9265.t88 Gene=g9265 Length=850
ATGATTAGTTACGATACACACACAAAATTAAAATCTTTTTATTCATCATTTTTGCCCTTT
CAGCTTCAATTTATAAAGAAATTCATTGAGAAATTCTTTGCATTTCGATTGTTAAGTATA
ACGGTTATTTCGTAATTTAAAAAAAGCGTAGTTGTCTTTCAATCCAAAAAACTGCAACTC
GTTCTTTTCGAACAATCCTTCAAAGAGGAAAGGTGTGTTTTCATAAAATTTATGTCTATC
ATTAATCGTAAATAATGGGTGCGTACAGATACGTTCAAGAGTTATATCGCAAAAAGCAGA
GCGATGTTCTTCGCTATTTGCTTCGAGTTAGATGCTGGCAATATCGTCAATTGACTAAAT
TGCATCGTGCTCCACGTCCATCACGTCCTGATAAAGCACGTCGTCTTGGTTATCGTGCAA
AGCAAGGATTTTTGATCTATCGCATTCGTGTTCGCCGTGGAGGTCGCAAACGTCCAGTAC
ACAAGGGATGCACATATGGCAAACCAAAAAGTCATGGTGTTAACCAATTGAAGCCATACA
GAAAGAACGTGTTGGTCGACGATTGGGAGGACTTCGTGTTCTCAATTCATACTGGGTCGC
ACAAGATGCTGCATTCAAATATTACGAAGTCATCTGCATCGATCCATTCCACAATGCTAT
TCGTCGTGATCCTAAAGTTAACTGGATTTGTAATGCTGTTCACAAGCATCGTGAATTACG
CGGACTTACATCTGCCGGAAAGAGCTCACGCGGTATTGGAAAAGGATACAGATATTCACA
AACTATTGGTGGCTCACGTCGTGCTGCATGGCGTCGAAAGAATCGCCTCCATCTCCGTCG
CTATCGTTAA
>g9265.t88 Gene=g9265 Length=198
MGAYRYVQELYRKKQSDVLRYLLRVRCWQYRQLTKLHRAPRPSRPDKARRLGYRAKQGFL
IYRIRVRRGGRKRPVHKGCTYGKPKSHGVNQLKPYRKNVLVDDWEDFVFSIHTGSHKMLH
SNITKSSASIHSTMLFVVILKLTGFVMLFTSIVNYADLHLPERAHAVLEKDTDIHKLLVA
HVVLHGVERIASISVAIV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9265.t88 | Gene3D | G3DSA:3.40.1120.10 | Ribosomal protein l15e | 1 | 101 | 1.2E-47 |
| 2 | g9265.t88 | PANTHER | PTHR11847:SF4 | 60S RIBOSOMAL PROTEIN L15 | 1 | 98 | 8.2E-47 |
| 3 | g9265.t88 | PANTHER | PTHR11847 | RIBOSOMAL PROTEIN L15 | 1 | 98 | 8.2E-47 |
| 1 | g9265.t88 | Pfam | PF00827 | Ribosomal L15 | 2 | 98 | 1.3E-37 |
| 7 | g9265.t88 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 133 | - |
| 8 | g9265.t88 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 134 | 156 | - |
| 6 | g9265.t88 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 157 | 198 | - |
| 10 | g9265.t88 | ProSitePatterns | PS01194 | Ribosomal protein L15e signature. | 46 | 69 | - |
| 11 | g9265.t88 | SMART | SM01384 | Ribosomal_L15e_2 | 2 | 135 | 7.4E-36 |
| 4 | g9265.t88 | SUPERFAMILY | SSF54189 | Ribosomal proteins S24e, L23 and L15e | 1 | 101 | 6.23E-41 |
| 9 | g9265.t88 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 134 | 156 | - |
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. There were no conditions that were differentially expressed