Description
This composite track depicts previously non-annotated alternative translation initiation sites (TISs) in a human monocytic cell line (THP-1) published by Jochen Hampe′s lab (Fritsch et al. 2012). Ribosome profiling of purmycin treated cells was used to identify translational start sites.
Display conventions
The subtrack "Reference Transcript" displays the analyzed transcript. The subtrack "Identified TIS" depicts the identified translation initiation sites (grey boxes). The subtrack "classified TIS" shows TISs, for which a start codon has been annotated (red boxes).
Methods
If more than one transcript per gene was available, the transcript with the most 5′ location of the annotated TIS and the longest 5′UTR was chosen as reference transcript. For TIS prediction, a neural network was trained on the ribosomal footprints observed at previously annotated AUG start codons. The predicted TIS were finally classified into one of four functional categories: annotated TIS, N-terminal protein extension, upstream ORF, or CDS-overlapping uORF.
Credits
These data were generated and analyzed by the laboratory of Prof. Dr. J. Hampe at the University Hospital Schleswig-Holstein, Kiel, Germany as part of the Virtual Liver Network (contact: Jochen Hampe). This track was constructed by Alexander Hermann at University Hospital Schleswig-Holstein, Kiel.
References
Fritsch, C., Herrmann, A., Nothnagel, M., Szafranski, K., Huse, K., Schumann, F., Schreiber, S., et al. (2012). Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting. Genome Res, 22(11), 2208–2218.
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