This track shows the genome-wide expression map of monkeypox virus. ORFs are selectively expressed at early, intermediate, or late times of infection. This is due to stage-specific viral promoters and transcription factors associated with the viral DNA-dependent RNA polymerase. ORFs are named according to the official nomenclature of orthopoxviruses.
ORFS are colored according to the time of their transcription: green for early genes, blue for intermediate genes, and red for late genes.
Expression data were obtained from ribosome profiling data from the Vacinia virus study: Deciphering poxvirus gene expression by RNA sequencing and ribosome profiling. The monkexpox data were annotated for similarity. The monkexpox genome is very similar to the vaccinia virus genome, and all orthopoxviruses share the same expression pattern and replication cycle.
The gene names follow the universal OPGXXX (OrthoPoxvirus Gene number XXX) convention published in Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes.
The raw data can be explored interactively with the Table Browser or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.
Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mpxvRivers/viralzoneGenes/viralzone.bb -chrom=NC_063383.1 -start=0 -end=100000 stdout
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.
Zhilong Yang, Shuai Cao, Craig A Martens, Stephen F Porcella, Zhi Xie, Ming Ma, Ben Shen, Bernard Moss Deciphering poxvirus gene expression by RNA sequencing and ribosome profiling J Virol 2015 Jul;89(13):6874-86.
Tatiana G Senkevich, Natalya Yutin, Yuri I Wolf, Eugene V Koonin, Bernard Moss Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes mBio 2021 Aug 31;12(4):e0149521