Dear All I'm Stefano Berto and I'm working in the Katja Nowick group as a PhD student. In the signature you can easily find my project.
Nowadays I'm working with Transcription factors and the differences between humans and closely related species. Thus I found very useful your accurate annotations. Unfortunately I detected an error downloading a sequence of ZNF717. This Zinc Finger can be easily found in catalogue: http://znf.igb.uiuc.edu/human/action/exploreView?type=locus&id=732 and also in your database, Blatting the sequences and find the locus in the Chromosome. The problem that I noticed is the protein sequence of ZNF717. From http://znf.igb.uiuc.edu/human/action/exploreView?type=locus&id=732 I checked the domains of the protein (KRAB, fingers etc) finding a correct annotation of the protein. But if I download the protein sequence there is an error. In fact, I tried to detect the Zinc Finger domains in the sequence download and I found some mistakes about some undetectable domains. Here I'm explaining the problem: http://znf.igb.uiuc.edu/human/action/exploreView?type=locus&id=732 Here there are the list of domains. I took this ZNF domain: YECNECGKSFHQKANLQKHQGIHTGEKP This is the 18th ZNF domain but I noticed the error in other motifs. Now I download the protein sequence from the same catalogue and I tried, with the alignment tool, to detect the sequence but unfortunately I couldn't. Thus I blatted the finger sequence in the UCSC website finding a 100% of identity with a locus in the Chr 3. It is completely inside the ZNF717. The ERROR is here. In fact I clicked in the browser and, as you understand if you are following my steps, the SEQUENCE in the browser is completely different: MNVMNVENPFIRRQIFRSIKVFTRGRN Moreover I double checked with the translation of the chromosome locus and it will give me the CORRECT zinc finger sequence (YECNECGKSFHQKANLQKHQGIHTGEKP). Moreover the Refseq in your database is the same that I had from the catalogue and it is wrong too. Thus I guess there is a mismatch between the database and the reference sequence that you can download. I got in one hand one plausible result but on the other hand a wrong reference sequence. Could you check the error? I hope you can understand the explanation. I did my best. By the way, if you need more information, don't hesitate to contact me. Looking forward to hear from you soon Best Regards Stefano -- Stefano Berto PhD student "TFome and Trancriptome Evolution" www.nowick-lab.info Universität Leipzig Härtelstrasse 16-18 04107 Leipzig Germany Phone: +49 341 97-16667 Mobile: +49 0162 7480640 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
