Based on the provided image of the MCPyV (Merkel cell polyomavirus) genome, it appears that ALTO is positioned between the LT (Large T antigen) and sT (small T antigen) regions. However, it’s not entirely clear from the diagram alone if ALTO is a distinct domain within sT, or if it’s a separate gene entirely.
In the literature, the ALTO protein (A novel T antigen Open Reading Frame) of MCPyV has been described as a unique feature of the virus. While its specific function and relationship to the other T antigens (LT and sT) are still a topic of research, it is indeed distinct from the canonical LT and sT proteins.
In short, based on the diagram and typical annotations for MCPyV, ALTO does not appear to be a part of sT; rather, it’s a distinct open reading frame (ORF) or protein. However, more detailed genomic annotations and experimental studies would be needed to definitively determine its relationship with other proteins encoded by the virus.
https://www.frontiersin.org/articles/10.3389/fmicb.2021.739695/full
JN707599.gtf
JN707599 Genbank gene 465 1190 . + . gene_id "VP2"; gene_type "protein_coding"
JN707599 Genbank transcript 465 1190 . + . gene_id "VP2"; transcript_id "tx-AEX86628.1"; gene_type "protein_coding"
JN707599 Genbank exon 465 1190 . + 0 gene_id "VP2"; transcript_id "tx-AEX86628.1"; gene_type "protein_coding"
JN707599 Genbank CDS 465 1190 . + 0 gene_id "VP2"; transcript_id "tx-AEX86628.1"; gene_type "protein_coding"
JN707599 Genbank gene 600 1190 . + . gene_id "VP3"; gene_type "protein_coding"
JN707599 Genbank transcript 600 1190 . + . gene_id "VP3"; transcript_id "tx-AEX86629.1"; gene_type "protein_coding"
JN707599 Genbank exon 600 1190 . + 0 gene_id "VP3"; transcript_id "tx-AEX86629.1"; gene_type "protein_coding"
JN707599 Genbank CDS 600 1190 . + 0 gene_id "VP3"; transcript_id "tx-AEX86629.1"; gene_type "protein_coding"
JN707599 Genbank gene 1156 2427 . + . gene_id "VP1"; gene_type "protein_coding"
JN707599 Genbank transcript 1156 2427 . + . gene_id "VP1"; transcript_id "tx-AEX86630.1"; gene_type "protein_coding"
JN707599 Genbank exon 1156 2427 . + 0 gene_id "VP1"; transcript_id "tx-AEX86630.1"; gene_type "protein_coding"
JN707599 Genbank CDS 1156 2427 . + 0 gene_id "VP1"; transcript_id "tx-AEX86630.1"; gene_type "protein_coding"
JN707599 Genbank gene 2503 5387 . - . gene_id "LT"; gene_type "protein_coding"
JN707599 Genbank transcript 5154 5387 . - . gene_id "LT"; transcript_id "tx1-AEX86632.1"; gene_type "protein_coding"
JN707599 Genbank exon 5154 5387 . - 0 gene_id "LT"; transcript_id "tx1-AEX86632.1"; gene_type "protein_coding"
JN707599 Genbank CDS 5154 5387 . - 0 gene_id "LT"; transcript_id "tx1-AEX86632.1"; gene_type "protein_coding"
JN707599 Genbank transcript 2503 4722 . - . gene_id "LT"; transcript_id "tx2-AEX86632.1"; gene_type "protein_coding"
JN707599 Genbank exon 2503 4722 . - 0 gene_id "LT"; transcript_id "tx2-AEX86632.1"; gene_type "protein_coding"
JN707599 Genbank CDS 2503 4722 . - 0 gene_id "LT"; transcript_id "tx2-AEX86632.1"; gene_type "protein_coding"
JN707599 Genbank gene 4827 5387 . - . gene_id "sT"; gene_type "protein_coding"
JN707599 Genbank transcript 4827 5387 . - . gene_id "sT"; transcript_id "tx-AEX86631.1"; gene_type "protein_coding"
JN707599 Genbank exon 4827 5387 . - 0 gene_id "sT"; transcript_id "tx-AEX86631.1"; gene_type "protein_coding"
JN707599 Genbank CDS 4827 5387 . - 0 gene_id "sT"; transcript_id "tx-AEX86631.1"; gene_type "protein_coding"JN707599.fasta
JN707599 CTTGTCTATATGCAGAAGGAGTTTGCAGAAAGAGCAGAGGAGCAAATGAGCTACCTCACTAAGGAGTGGT TTTTATACTGCAGTTTCCCGCCCTTGGGATCTGCCCTTAGATACTGCCTTTTTTGCTAATTAAGCCTCTT AAGCCTCAGAGGCCTCTCTCTTTTTTTTCCAGAGGCCTCGGAGGCTAGGAGCCCCAAGCCTCTGCCAACT TGAAAAAAAAAAGTCACCTAGGCAGCCAAGTTGTGGTTACATGATTGAACTTTTATTGCTGCAGGGTTTC TGGCATTGACTCATTTCCTGGAGAGGCGGAGTTTGACTGATAAACAAAACTTTTTTTCTTTCTGTTTGGG AGGGAGACGGAAGACTCTTAACTTTTTTTCAACAAGGGAGGCCCGGAGGCTTTTTTTTCTCTTACAAAGG GAGGAGGACATTAAAAGAGTAAGTATCCTTATTTATTTTTCAGGATGGGGGGCATCATCACACTGCTGGC CAATATTGGTGAAATTGCTACTGAACTAAGTGCCACCACAGGAGTAACTTTGGAAGCTATTCTTACAGGA GAAGCTTTAGCAGCTTTGGAAGCAGAGATCTCCAGTTTAATGACAATTGAGGGTATTTCTGGCATTGAGG CTTTAGCTCAACTTGGGTTCACAGCTGAACAGTTTTCAAATTTCTCATTAGTGGCTTCTTTGGTTAACCA AGGTTTAACTTATGGCTTCATTCTCCAAACTGTTAGTGGTATAGGCTCTCTAATAACTGTGGGGGTGAGG TTGTCACGCGAGCAAGTGTCACTTGTAAAGAGGGATGTTTCGTGGGTAGGTAGTAATGAGGTTTTGAGGC ATGCACTTATGGCCTTTAGCCTAGATCCTCTGCAGTGGGAAAATAGCTTGCTGCATTCTGTGGGGCAAGA TATTTTTAATTCTTTATCTCCTACCTCTAGGCTGCAGATACAATCAAACCTAGTGAATCTGATACTAAAT AGCCGGTGGGTCTTTCAGACAACTGCTTCTCAGAATCAGGGCCTTTTATCAGGAGAGGCTATATTAATTC CTGAACATATAGGAGGAACTCTGCAGCAGCAAACTCCAGATTGGCTTCTTCCTCTGGTACTAGGCCTTAG TGGATATATTTCTCCTGAATTACAAGTAATTGAAGATGGCACCAAAAAGAAAAGCATCATCCACCTGTAA AACACCCAAAAGGCAATGTATACCTAAGCCGGGATGCTGCCCTAATGTTGCCTCAGTTCCAAAACTGCTT GTTAAAGGAGGAGTGGAAGTATTATCTGTGGTTACTGGAGAAGATAGCATTACCCAAATTGAGTTGTATT TGAATCCAAGAATGGGAGTTAATTCCCCTGATCTTCCTACTACTTCAAACTGGTATACTTATACTTATGA CCTGCAGCCAAAGGGATCATCTCCAGATCAGCCCATCAAGGAAAATTTGCCAGCTTACAGTGTGGCAAGA GTGTCTCTGCCAATGCTAAATGAGGATATTACCTGTGACACATTGCAGATGTGGGAGGCAATATCTGTTA AAACAGAAGTAGTTGGAATAAGTTCTTTAATTAATGTTCATTATTGGGACATGAAAAGAGTTCATGATTA TGGTGCTGGTATTCCTGTGTCAGGGGTAAATTACCATATGTTTGCCATTGGGGGAGAACCTCTGGATTTG CAAGGCCTAGTTTTAGATTACCAGACTGAGTATCCAAAAACTACAAATGGTGGGCCTATTACAATTGAAA CTGTATTGGGAAGAAAAATGACACCTAAAAATCAGGGCCTAGATCCACAAGCTAAAGCAAAATTAGATAA AGATGGAAATTATCCTATAGAAGTATGGTGTCCTGATCCTTCTAAAAATGAAAACAGTAGATACTATGGG TCTATTCAGACAGGCTCTCAGACTCCTACAGTTCTTCAATTTAGTAATACTCTAACTACTGTCCTTTTAG ATGAGAATGGAGTGGGCCCTCTATGCAAAGGAGATGGCCTATTTATTAGCTGTGCAGACATAGTGGGGTT TCTGTTTAAAACCAGTGGAAAAATGGCTCTTCATGGGTTGCCTAGATATTTTAATGTTACTTTGAGAAAA AGATGGGTGAAAAACCCCTACCCAGTAGTTAATTTAATAAACTCACTCTTCAGCAACTTAATGCCAAAAG TGTCAGGCCAACCTATGGAAGGAAAAGATAATCAGGTAGAAGAGGTTAGAATATATGAGGGGTCAGAACA ATTACCTGGTGATCCTGATATTGTCAGATTTTTAGATAAATTTGGGCAGGAGAAAACTGTTTACCCAAAG CCCTCTGTTGCCCCAGCAGCAGTAACATTCCAAAGTAATCAGCAGGATAAGGGCAAGGCGCCACTGAAAG GACCTCAAAAGGCCTCTCAAAAAGAAAGCCAAACACAAGAATTATGAGAATTATTTCATGCATTCCTATT CAGTTAAGTAGGCCCCAGAAAAACAAACACAGGAAATATGAAGCAGATGCCTTTATTGAGAAAAAGTACC AGAATCTTGGGTTTCTTCAGTTTCCTCAGGGCCCTCTTCCTCAATAAGAATATTGAGCAGAGGGTCCTGA CCAGCTTCTACATTTTCTATCATTTGACAAAATTTACCATATGATATTTCACTCTGTAAAATTTGCTTCC AGTTTTTAATTTCTTCTTGTAAGCAAGGCTTAAAGGTTGTATCAGGCAAGCACCAAATAAGACAAAGCAA TAAAGTGGTTCCACTTTGAAGAATTCTTCTTTTTCTTATTTCCATGTTCTGATCCAGGGAATCTCTTAGA TTTGCCTTTGGGGAAAAGTGTAAAGTATAACTAAATCTTGCTATTAATGTTTTGGGAATAAAATAATCAT TAGCAGTAACAATACAAGGAGGAAAAATCTGATGCTTTTTATTCACATGCTTCTTCTCTAAGCTTACAGC TACAGCACCATCTAGATGATCTCTTAAGTTATCAAGGTTATTTATTCCTTGCCCTGGTTGCAGATCTTTA TTTAGGCTATTTTGCCCTTTCACATCCTCAAAAACAACCATAAATTTATCCAAAGCACATCCTAGTTCAA AAGGCAGTTTATCAGATGGACAGTTTATATTCAAGGCCTTCCCTTCTAGCAAATCTATTAAGGCTGCAGC AAAGCTTGTTTTTCCACTGTTAATAGGCCCTTTAAACCAAATGTTTCTATACTTAGGTATATTCTCTGTT AATAATTGAATAATTTTCTGCAGCTTCTTTTCAAACTCTTCAAATAAGCAGCAGTACCAGGCCACACCAC CCATATAATACAGTAGATCTATTGTATCTAAATCTCTTAATCTCTCTAGGTGCTTCTTAAACTTCTTACA TAGCATTTCTGTCCTGGTCATTTCCAGCATCTCTAACCTCCTTTTGGCTAGAACAGTGTCTGCGGCTTGT TGGCAAATGGTTTTCTGAGATTTAGATTCATAAAATAGCTTAGCATTAGAATGATGAGCCTCATGAGCCT TGTGAGGTTTGAGGCGAGATCTGTTTTCACACTTTTGGCAAGGAAATGGTTTTGCAAAGTCTAGATAATG GGCTAAGATAATAAAGTGGTCGTCTAGCTCATATTCACAAGCAAATTCAGCAACTAAATTCCAATTACAG CTGGCCTCTTTTTCTTTTTCTTGAAATTCATAATTGAGCAGTGGCTTATTCTCTTGCAGTAATTTGTAAG GGGGCTTGCATAAATTATTATACATTTCAGGCATCTTATTCACTCCTTTACAAATTAAAAAGCTTATAGT GCAGAAGGTAGAGCAAAAATTCTTAATAGCAGATACTCTATGCTTTGATAAAGTTATAAACAATAAAATA CATCCTAATTCACAGGCATGCCTGCTTTTAAAATCAACTTTAAATTTCTCAATCTTATCATATAACTCTA TAGCTTTATCAGAAGTAGTATAAATGGCAAAACAACTTACTGTTTTATTACTATATACAGCATGGCTAAG ATAATCAGAAAGATCAATAGGAAAATCAGTAGGAACAGGAGTTTCTCTGTTCTTTTTTGGCTTTGGTGGA GTGCTTGTAAAACTTGCTGAACTAGCAGAGCTTGCAGAGCTTCGGGACCCCCCAAATTTTCGCTTTCTTG AGAATGGAGGAGGGGTCTTCGGGGTGGTGAAGGAGGAGGATCTGTATTCCTCATCTGTAAACTGAGATGA CGAGGCCTCCTCGGCAGAGGAAGACGGGGGCTGCCGGGGCGAGCTTCTTGAGGAGGGGGGCTCCTCAGGC TCCTCAGAGGACGAGGGAGGCTCAGGGGAGGAAAGTGATTCATCGCAGAAGAGATCCTCCCAGGTGCCAT CCGTTCTGGAAGAATTTCTAGGTACACTGGTTCCATTGGGTGTGCTGGATTCTCTTCCTGAATTGGTGGT CTCCTCTCTGCTACTGGATCCAGAGGATGAGGTGGGTTCCTCATGGTGTTCGGGAGGTATATCGGGTCCT CTGGACTGGGAGTCTGAAGCCTGGGACGCTGAGAAGGACCCATACCCAGAGGAAGAGCTCTGGCTGTGGG GTGGTGAGCTTCCACTGGGGGCTCCCCTGGATGCATTGGAGGAAGGCTTTCTGGATCTTGAGTTGGTCCC GTGTGGATTGGGCCCATATTCGTATGCCTTCCCGAAGCTGAATCCTCCTGATCTCCACCATTCTTTGAAT TTAGTGGTCCCATATATAGGGGCCTCGTCAACCTAGATGGGAAAGTACAGAAAATCTGTCATAAATAACC TTTCTTTGATATTTTGCCTTATAGACTTTTCCATATCTAATACTTACAGAGGAAGGAAGTAGGAGTCTAG AAAAGGTGCAGATGCAGTAAGCAGTAGTCAGTTTCTTCTAAAGTTTTTTGCCACCAGTCAAAACTTTCCC AAGTAGGAGGAAATCCAAACCAAAGAATAAAGCACTGATAGCAAAAACACTCTCCCCACGTCAGACAGTT TTTTTGCTTTAAAGTTTTTAGACTACAATGCTGGCGAGACAACTTACAGCTAATACAAGCGCACTTAGAA TCTCTAAGTTGCTTAAGCATGCACCCAGGACCTCTGCAAAATCTAGCATTATATCCACTTTGCATATAAT CCTTTAAAGTTCCATATTCTTCCCAAGGAAATTTTGTACTGACCTCATCAAACATAGAGAAGTCACTTCT GAGCTTGTGGATATTTTGCTGGAATTTGCTCCAAAGGGTGTTCAATTCCATCATTATAACAGGATTTCCC CCTTTATCAGGGTGATGCTTTAAGCAGCTTCTTTTGAAAGCAGCTTTCATCAGAGGGATGTTGCCATAAC AATTAGGAGCAATCTCTAAAAGCTTGCAGAGAGCCTCTCTTTCTTTCCTATTTAGGACTAAATCCAT
| title | treatment | time |
|---|---|---|
| untreated_DonorI | untreated | Day 0 |
| untreated_DonorII | untreated | Day 0 |
| p601_d3_DonorII | mCherry control | Day 3 |
| p604_d3_DonorII | sT | Day 3 |
| p601_d8_DonorII | mCherry control | Day 8 |
| p604_d8_DonorII | sT | Day 8 |
| p601_d3_DonorI | mCherry control | Day 3 |
| p604_d3_DonorI | sT | Day 3 |
| p601_d8_DonorI | mCherry control | Day 8 |
| p604_d8_DonorI | sT | Day 8 |
| p600_d3_DonorII | GFP control | Day 3 |
| p605_d3_DonorII | LTtr | Day 3 |
| p600_d8_DonorII | GFP control | Day 8 |
| p605_d8_DonorII | LTtr | Day 8 |
| p600_d3_DonorI | GFP control | Day 3 |
| p605_d3_DonorI | Lttr | Day 3 |
| p600_d8_DonorI | GFP control | Day 8 |
| p605_d8_DonorI | Lttr | Day 8 |
| p602_d8_DonorII | LT | Day 8 |
| p602_d8_DonorI | LT | Day 8 |
| p600and601_d12_DonorI | GFP+mCherry control | Day 12 |
| p604and605_d12_DonorI | sT+LTtr | Day 12 |
| p600and601_d9_DonorII | GFP+mCherry control | Day 9 |
| p604and605_d9_DonorII | sT+LTtr | Day 9 |
| p602_d3_DonorI | LT | Day 3 |
| p602_d3_DonorII | LT | Day 3 |
| p602and604_d3_DonorI | sT+LT | Day 3 |
| p602and604_d3_DonorII | sT+LT | Day 3 |
-
untreated
-
p602 LT *
-
p687 LT K331A *
-
p605 LTtr * (vs. p600 GFP control)
-
p604 sT
-
p602+604 LT+sT (vs. p601 mCherry control)
-
p604+p605 sT+LTtr (vs. GFP+mCherry control p601+p600)
Filtering RNA-seq analysis results and Workbook Creation with R
# Load required libraries
if(!requireNamespace("readxl", quietly = TRUE)) install.packages("readxl")
if(!requireNamespace("dplyr", quietly = TRUE)) install.packages("dplyr")
if(!requireNamespace("writexl", quietly = TRUE)) install.packages("writexl")
if(!requireNamespace("openxlsx", quietly = TRUE)) install.packages("openxlsx")
library(readxl)
library(dplyr)
library(writexl)
library(openxlsx)
setwd("/media/jhuang/Seagate Expansion Drive/Data_Denise_RNASeq/results_24samples/featureCounts/degenes_2021")
# Read the data from the specific sheet
data <- read_excel("degenes_replicates.xls", sheet = "p604_d3_vs_p601_d3-all")
print(data, n = 10, width = Inf)
# Filter the data
#filtered_data <- data %>%
# filter(padj < 0.05, log2FoldChange >= 2)
upregulated_genes <- data %>%
filter(padj < 0.05, log2FoldChange >= 2)
dim(upregulated_genes)
downregulated_genes <- data %>%
filter(padj < 0.05, log2FoldChange <= -2)
dim(downregulated_genes)
# Create a new Excel workbook
wb <- createWorkbook()
# Add sheets with data
addWorksheet(wb, "Up-regulated")
writeData(wb, "Up-regulated", upregulated_genes)
addWorksheet(wb, "Down-regulated")
writeData(wb, "Down-regulated", downregulated_genes)
# Save the workbook
saveWorkbook(wb, "sT_d3_up_and_down.xlsx", overwrite = TRUE)
data <- read_excel("p604_vs_p601_d8.xls", sheet = "p604_d8_vs_p601_d8-all")
print(data, n = 10, width = Inf)
upregulated_genes <- data %>%
filter(padj < 0.05, log2FoldChange >= 2)
dim(upregulated_genes)
downregulated_genes <- data %>%
filter(padj < 0.05, log2FoldChange <= -2)
dim(downregulated_genes)
# Create a new Excel workbook
wb2 <- createWorkbook()
# Add sheets with data
addWorksheet(wb2, "Up-regulated")
writeData(wb2, "Up-regulated", upregulated_genes)
addWorksheet(wb2, "Down-regulated")
writeData(wb2, "Down-regulated", downregulated_genes)
# Save the workbook
saveWorkbook(wb2, "sT_d8_up_and_down.xlsx", overwrite = TRUE)