[ensembl-dev] missing transcripts

[Caffrey, Daniel]

Hi Magali,

If Ensembl 75 is using refseq sequences from December this probably explains the missing refseqs. However, the genbank/ENA accessions (JX682706, JX682707, and JX682708)  were released in Aug 2013 . As the track is named refseq/ ENA I would expect them to be included (assuming version 75 is using ENA from December '13).

Thanks,

Daniel




On Feb 28, 2014, at 6:44 AM, mag <mr6 at ebi.ac.uk<mailto:mr6 at ebi.ac.uk>> wrote:

Hi Daniel,

The two RefSeq entries you are referring to have been last updated early February 2014 and mention a paper from late January 2014.
Could it be that these entries have only been recently created, hence would not have made it in our database at the time of update?

The RefSeq track displayed in Ensembl 75 was updated end of last year, so any more recent RefSeq entries would not be included here.


Regards,
Magali

On 27/02/2014 19:15, Caffrey, Daniel wrote:
Hi,

Does anyone know why the following refseq sequences/alignments do not appear in version 75 (or other versions) of the cDNAs (Refseq/ENA) track on the location tabs

REFSEQ: NR_110420
mouse 1:150159043-150164948



REFSEQ: NR_110375
human: 12:125509989-125511939

There appear to be similar issues with other transcripts - They are all lincRNAs and perhaps this is the reason?

 Related to this, I know there are at least  3 splice variants/transcripts for the mouse gene in genbank (JX682706, JX682707, and JX682708) but Ensembl/gencode only lists a single transcript ENSMUST00000181308. Presumably cDNA data is sufficient evidence for inclusion within gencode?

Thanks

Daniel





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