General information for g2840.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L15, mitochondrial.
Parent gene
- The parent gene g2840 is located on chr_3: 20509267..20510888 (+ 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_3 | g2840 | g2840.t3 | isoform | g2840.t3 | 20508007 | 20509267 |
| chr_3 | g2840 | g2840.t3 | exon | g2840.t3.exon1 | 20508007 | 20508009 |
| chr_3 | g2840 | g2840.t3 | exon | g2840.t3.exon2 | 20508284 | 20508485 |
| chr_3 | g2840 | g2840.t3 | cds | g2840.t3.CDS1 | 20508356 | 20508485 |
| chr_3 | g2840 | g2840.t3 | exon | g2840.t3.exon3 | 20508543 | 20509267 |
| chr_3 | g2840 | g2840.t3 | cds | g2840.t3.CDS2 | 20508543 | 20509267 |
| chr_3 | g2840 | g2840.t3 | TTS | g2840.t3 | 20509310 | 20509310 |
| chr_3 | g2840 | g2840.t3 | TSS | g2840.t3 | NA | NA |
Sequences
>g2840.t3 Gene=g2840 Length=930
GAGACGATAATTCATCAAATTTTCAAGAAATTAAATTGTAATAAGCTAAGAATAATACAA
TAAACATCAACAAAGATGGCAAGCTTGAAACATACATCAGAAAAAGCTCTTCAGATGCTT
CGTTCTTTACCGAGATTGTCATTAGCAAATATTCGTGATAATCCTCATTCTAGAATAAAG
ACTAAGCGAGGAAGAGGACAACACCGCGGAGATTTTCATGGAAATGGTCAAAAGAGATGG
ACAGTTCTTCGATTGGGTTACGATTGCAGCAACTCTCCTTTTTATCTACGATTCAAATAT
GAGCCATATTATCAAGGACATCATTTAAGACGACAGTATCCACCAATTACATTGAAAACT
CTTCAAATGCTTATTGATAGCAATCGTCTTGACACTTCACGACCAATTGATGTTGCATCT
CTCTGCACAACCGGTCTTTTTCAAATATTCCCAGACGAGAAACAGTTTGGTTTTCAATTG
ATTGATGAAGGAGCTGAATGTTTCAAAGCAAAGATCAATATTGAAGTACAGCATGCAAGT
GAATTAGTTATTGCAGCAATTGAGAAAAATGGTGGTGTCATTAGAACAGCATATTATGAT
CAGAAAGCATTACATGCTCTTAGAGATCCTAAAAAATTCTTTGAAAGAGGTTTGCCAATT
CCTAGAAGAATGATTCCACCTCAAGATGCAGTCGAATATTATTCAAACCCAAAAAATCGT
GGTTATCTTGCAGATCCAGAAGCTATTTCACATGAACGTTTAGTTCTTGCTCAAAAGTAT
GGCTACAAATTACCCAAAATTGAAGATGATCCACAATACAATATGCTCATTGAAACGAAA
GATCCACGTCAGATTTTCTATGGTCTTGAACCGGGTATTGTCGTAAATTTAAAAGATAAA
TGCATTATTAAACCTAAAGTAGACGTTTAA
>g2840.t3 Gene=g2840 Length=284
MASLKHTSEKALQMLRSLPRLSLANIRDNPHSRIKTKRGRGQHRGDFHGNGQKRWTVLRL
GYDCSNSPFYLRFKYEPYYQGHHLRRQYPPITLKTLQMLIDSNRLDTSRPIDVASLCTTG
LFQIFPDEKQFGFQLIDEGAECFKAKINIEVQHASELVIAAIEKNGGVIRTAYYDQKALH
ALRDPKKFFERGLPIPRRMIPPQDAVEYYSNPKNRGYLADPEAISHERLVLAQKYGYKLP
KIEDDPQYNMLIETKDPRQIFYGLEPGIVVNLKDKCIIKPKVDV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2840.t3 | Gene3D | G3DSA:3.100.10.10 | - | 89 | 234 | 0 |
| 2 | g2840.t3 | PANTHER | PTHR12934 | 50S RIBOSOMAL PROTEIN L15 | 6 | 236 | 0 |
| 3 | g2840.t3 | PANTHER | PTHR12934:SF11 | 39S RIBOSOMAL PROTEIN L15, MITOCHONDRIAL | 6 | 236 | 0 |
| 1 | g2840.t3 | Pfam | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | 49 | 170 | 0 |
| 4 | g2840.t3 | SUPERFAMILY | SSF52080 | Ribosomal proteins L15p and L18e | 33 | 177 | 0 |
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:0015934 | large ribosomal subunit | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02876 (large subunit ribosomal protein L15)
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.
