I came across the problem when I looked for the VEGFR3 sequence in NCBI Nucleotide. The mRNA sequence (e.g. Accession: NM_182925.4 for transcript variant 1) are different at several sites compared to the complete CDS sequence (e.g. Accession: AY233383.1 for long form). Does anyone know the reason for this inconformity?
Yes, the sequence may come from different individuals. But there are 11bp differences within about 4000bp CDS region. Do you think the frequency of this polymorphism is normal?
Thank you for your answer, Mr Burzynski. In my studies with receptor tyrosine kinases, I have not noticed similar issue in other family members. That is why I asked. Seems that is my ignorant. Anyway, at least VEGFR3 is sort of special within its family in this aspect.
The submission date of AY233383.1 to GenBank was 09-APR-2003. "NM_" codes refers to manually and frequently curated sequences by GenBank-NCBI staff and are named as RefSeq (http://www.ncbi.nlm.nih.gov/books/NBK21091/). The NM_182925 sequence is at version 4 (NM_182925.4, "dot 4") with last update in 11-MAY-2014. The 5'UTR and 3'UTR are much more evident in RefSeq than AY233383.1. Of course, consider polymorphism but also pay attention to curated info.
Hi, I agree with Francis Nunes. You should trust much more the NM sequence than the old one.
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