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Old 01-04-2012, 11:48 AM   #1
husamia
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Location: cinci

Join Date: Apr 2010
Posts: 66
Default NCBI RefSeq "unclassified transcription discrepancy"

I wasn't sure if this forum would have discussed this before or would be a good place to discuss but I am sure some may be able to help and others may benifit. I searched and couldn't find anything.

I encountered some genes where the translation produices an unexpetedly stop codon. I pay attention to the details and I found that the NCBI record lists the following note in the genbank file


mRNA join(1..176,326..467,949..1102,4444..4605,4819..4951,
5672..5765,6325..6448,7339..7521,8239..8512,10329..10447,
12266..13019)
/gene="UNC93B1"
/gene_synonym="MGC126617; Unc-93B1; UNC93; UNC93B"
/product="unc-93 homolog B1 (C. elegans)"
/exception="unclassified transcription discrepancy"
/note="Derived by automated computational analysis using
gene prediction method: BestRefseq."
/transcript_id="NM_030930.2"
/db_xref="GI:45580708"
/db_xref="GeneID:81622"
/db_xref="HGNC:13481"
/db_xref="HPRD:12191"
/db_xref="MIM:608204"
CDS join(81..176,326..467,949..1102,4444..4605,4819..4951,
5672..5765,6325..6448,7339..7521,8239..8512,10329..10447,
12266..12577)
/gene="UNC93B1"
/gene_synonym="MGC126617; Unc-93B1; UNC93; UNC93B"
/exception="unclassified translation discrepancy"
/note="Derived by automated computational analysis using
gene prediction method: BestRefseq."
/codon_start=1
/product="protein unc-93 homolog B1"
/protein_id="NP_112192.2"
/db_xref="GI:45580709"
/db_xref="GeneID:81622"
/db_xref="HGNC:13481"
/db_xref="HPRD:12191"
/db_xref="MIM:608204"

I though this was an error in my software but it turns out this is a known problem notice "unclassified translation discrepancy"

I need to get the translation correctly and I can't figure out what went wrong. Is there problem in the consensus sequence that produces this stop codon or what?

Where does the consensus sequence come from and why would it have this discrepancy which apparently already known.
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