General information for g9265.t41
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.t41 | isoform | g9265.t41 | 1368153 | 1369667 |
| chr_1 | g9265 | g9265.t41 | exon | g9265.t41.exon1 | 1368153 | 1368571 |
| chr_1 | g9265 | g9265.t41 | TTS | g9265.t41 | 1368157 | 1368157 |
| chr_1 | g9265 | g9265.t41 | cds | g9265.t41.CDS1 | 1368187 | 1368571 |
| chr_1 | g9265 | g9265.t41 | exon | g9265.t41.exon2 | 1368771 | 1369078 |
| chr_1 | g9265 | g9265.t41 | cds | g9265.t41.CDS2 | 1368771 | 1369057 |
| chr_1 | g9265 | g9265.t41 | exon | g9265.t41.exon3 | 1369217 | 1369237 |
| chr_1 | g9265 | g9265.t41 | exon | g9265.t41.exon4 | 1369456 | 1369667 |
| chr_1 | g9265 | g9265.t41 | TSS | g9265.t41 | NA | NA |
Sequences
>g9265.t41 Gene=g9265 Length=960
ATGATTAGTTACGATACACACACAAAATTAAAATCTTTTTATTCATCATTTTTGCCCTTT
CAGCTTCAATTTATAAAGAAATTCATTGAGAAATTCTTTGCATTTCGATTGTTAAGTATA
ACGGTTATTTCGTAATTTAAAAAAAGCGTAGTTGTCTTTCAATCCAAAAAACTGCAACTC
GTTCTTTTCGAACAATCCTTCAAAGAGGAAAGATAGACGATTTATAAATACAGGTCTATC
ATTAATCGTAAATAATGGGTGCGTACAGATACGTTCAAGAGTTATATCGCAAAAAGCAGA
GCGATGTTCTTCGCTATTTGCTTCGAGTTAGATGCTGGCAATATCGTCAATTGACTAAAT
TGCATCGTGCTCCACGTCCATCACGTCCTGATAAAGCACGTCGTCTTGGTTATCGTGCAA
AGCAAGGATTTTTGATCTATCGCATTCGTGTTCGCCGTGGAGGTCGCAAACGTCCAGTAC
ACAAGGGATGCACATATGGCAAACCAAAAAGTCATGGTGTTAACCAATTGAAGCCATACA
GGAACGTGTTGGTCGACGATTGGGAGGACTTCGTGTTCTCAATTCATACTGGGTCGCACA
AGATGCTGCATTCAAATATTACGAAGTCATCTGCATCGATCCATTCCACAATGCTATTCG
TCGTGATCCTAAAGTTAACTGGATTTGTAATGCTGTTCACAAGCATCGTGAATTACGCGG
ACTTACATCTGCCGGAAAGAGCTCACGCGGTATTGGAAAAGGATACAGATATTCACAAAC
TATTGGTGGCTCACGTCGTGCTGCATGGCGTCGAAAGAATCGCCTCCATCTCCGTCGCTA
TCGTTAAAATGGAAATACACATTAAATCGATTTATTTTGTGTATATTGTTATAAACATCT
TAACAATTTTTTTCAAAAATGAATAAATTTCATATATCAAAAACAATATGAAACTCAAAA
>g9265.t41 Gene=g9265 Length=223
MGAYRYVQELYRKKQSDVLRYLLRVRCWQYRQLTKLHRAPRPSRPDKARRLGYRAKQGFL
IYRIRVRRGGRKRPVHKGCTYGKPKSHGVNQLKPYRNVLVDDWEDFVFSIHTGSHKMLHS
NITKSSASIHSTMLFVVILKLTGFVMLFTSIVNYADLHLPERAHAVLEKDTDIHKLLVAH
VVLHGVERIASISVAIVKMEIHIKSIYFVYIVINILTIFFKNE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9265.t41 | Gene3D | G3DSA:3.40.1120.10 | Ribosomal protein l15e | 1 | 100 | 6.0E-48 |
| 2 | g9265.t41 | PANTHER | PTHR11847:SF4 | 60S RIBOSOMAL PROTEIN L15 | 1 | 98 | 5.6E-47 |
| 3 | g9265.t41 | PANTHER | PTHR11847 | RIBOSOMAL PROTEIN L15 | 1 | 98 | 5.6E-47 |
| 1 | g9265.t41 | Pfam | PF00827 | Ribosomal L15 | 2 | 98 | 1.5E-37 |
| 9 | g9265.t41 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 132 | - |
| 12 | g9265.t41 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 133 | 155 | - |
| 6 | g9265.t41 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 156 | 175 | - |
| 11 | g9265.t41 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 176 | 197 | - |
| 8 | g9265.t41 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 198 | 202 | - |
| 10 | g9265.t41 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 220 | - |
| 7 | g9265.t41 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 221 | 223 | - |
| 15 | g9265.t41 | ProSitePatterns | PS01194 | Ribosomal protein L15e signature. | 46 | 69 | - |
| 16 | g9265.t41 | SMART | SM01384 | Ribosomal_L15e_2 | 2 | 134 | 2.1E-37 |
| 4 | g9265.t41 | SUPERFAMILY | SSF54189 | Ribosomal proteins S24e, L23 and L15e | 1 | 98 | 4.51E-41 |
| 14 | g9265.t41 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 133 | 155 | - |
| 13 | g9265.t41 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 201 | 220 | - |
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.
