[ensembl-dev] missing transcripts

[Daniel Barrell]

Hi Daniel,

e!75 currently contains RefSeq data from a dump that the NCBI did for us 
on November 14th 2013. I've just looked at the human gff files and they 
do not include NR_110375

All the best

Daniel

On 28/02/14 14:39, Caffrey, Daniel wrote:
> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing listDev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog:http://www.ensembl.info/
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info: 
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140228/e509ffd4/attachment.html>