Question: Refseq Error: Insufficient Same-Species Transcript Support
gravatar for Woa
9.1 years ago by
United States
Woa2.8k wrote:

I've encountered a few supressed RefSeq entries like this

which tells that : "This RefSeq was temporarily suppressed because currently there is insufficient same-species transcript support"

Can somebody tell about the reason of withholding in some more details?

Thanks in advance


sequence refseq error genbank • 1.1k views
ADD COMMENTlink written 9.1 years ago by Woa2.8k
gravatar for Neilfws
9.1 years ago by
Sydney, Australia
Neilfws49k wrote:

You can see more information by clicking through to the sequence record. One section reads:

Sequence Note: This RefSeq record was created from genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by transcript alignments and orthologous data.

In other words, there is no single full-length transcript which aligns to the genome, but there are partial transcripts which align across the gene.

Chapter 18 of the NCBI Handbook describes in detail the RefSeq annotation process. It states:

A RefSeq record is suppressed if it is found to represent a transcribed repeat element, to be derived from the wrong organism (i.e., the INSDC sequence it was based on has incorrect organism annotation), or not to represent a "gene". Records determined to represent an incomplete sequence, such as a partial protein sequence or an incompletely spliced transcript, are temporarily suppressed until more complete sequence data are available. Suppressed records can still be retrieved and will have a disclaimer appearing on the query result document summary (Figure 3a). A suppressed record is not included in BLAST databases, in the calculation of related sequences, in the BLink display (BLink are pre-computed protein BLAST results), or in RefSeq FTP releases.

ADD COMMENTlink written 9.1 years ago by Neilfws49k

Thanks neilfws !!!

ADD REPLYlink written 9.1 years ago by Woa2.8k

You're welcome. Votes are a good way to show appreciation :)

ADD REPLYlink written 9.1 years ago by Neilfws49k
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