I tried designing primers for ELANE gene and came up with the following two sequences in in-silico PCR:
- >chr19:855442+856209 768 bp size
- >chr19_KI270868v1_alt:34328+35095 768 bp size.
Both the sequences are of the same size and 100% homologous. Does this mean the second is a pseudogene of the first? However this was seen for only two exon sequences while the remaining exons had no issues.
Thank you in advance.
Ziguo Zhang
These two are actually the same one (same locus). The second one is an alternative genome assembly during genome sequencing project.
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Frederic Lepretre
Hi Arun,
as Ziguo said, this is the same gene. Using blast with command lines manner on only one genome will give you only one position. Sometimes databases keep old data without purging them. use an other in-silico PCR website and see what will happen (UCSC, NCBI...).
fred
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