Misleading alias nomenklatur of STS marker
Dr. Thorsten Läufer
Dear UCSC Genome Browser Team,
I have a question regarding the nomenclature of the STS marker CHLC.GATA30B10. In both hg19 and hg38, the name D4S2370 is given for this marker on chromosome 5. According to our understanding, D4 requires a localization on chromosome 4. Is there a reason for the different nomenclature such as a subsequent correction of the localization or is the name just incorrectly assigned?
Kind regards / Mit freundlichen Grüßen
Thorsten Läufer
Jairo Navarro Gonzalez
Hello,
Thank you for using the UCSC Genome Browser and sending your inquiry.
The STS Markers track was last updated in 2015, and NCBI deleted the UniSTS database. The best solution would be to contact the author of the GenBank entry:
The contact information for Jeff Murray can be found on the following website:
If you contact Jeff Murray with your inquiry, could you also CC us in the email so we can update the track?
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
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Dr. Thorsten Läufer
Dear Professor Murray,
I hope this message finds you well.
My name is Thorsten Läufer, I am Head of Production at the FISH probe manufacturer MetaSystems Probes GmbH in Germany. I would like to ask you questions about an STS marker that was published under your name in GenBank in 1997: GATA30B10. The administrators of the UCSC Genome Browser referred me to you (the email history is attached).
https://www.ncbi.nlm.nih.gov/nuccore/G08352?report=GenBank
Our company uses the information on the position of STS markers from the UCSC Genome Browser as a reference to clarify the localization of the FISH probes on our probe maps for our customers. After a map revision, the marker GATA30B10 was newly entered on Chromosome 5 under its alias D4S2370 entered in UCSC. Two customers may have correctly noted that the marker name D4S2370 actually indicates a localization on chromosome 4.
My questions: Is the alias name D4S2370 simply wrong, perhaps due to a later annotation error? Or was there possibly a change of localization after a name was assigned? Unfortunately, I do not know the originator of the designation D4S2370.
In general, it is a pity that NCBI has stopped updating and maintaining the STS database. We, our customers and ultimately the patients still benefit from your work, even if it dates back decades.
Kind regards / Mit freundlichen Grüßen
Thorsten Läufer
_____________________________________________________________
Dr. Thorsten Läufer | Head of Production DNA-Probes
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tlae...@metasystems-probes.com
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