[Genome] rmsk annotation

[Adam Auton]

Hi Brooke,
    Many thanks for your reply. That's exactly the information I needed! 
The Tigger2a repeat seems to be stored in RepBase as MER28. It's 
interesting that two databases don't share common ID names. Maybe it's 
worth publishing a file that maps UCSC repName to RepBase ID?

Regards,

Adam

Brooke Rhead wrote:
> Hi Adam,
>
> When we construct the rmsk table we use the most current RepBase 
> library that is available.  The hg17 rmsk table was created in 2004 
> and used the RepBase8.12 library, which can be found on the GIRI web 
> site archives, here: http://www.girinst.org/server/archive/ 
> (accessible if you are a registered user).
>
> One of our engineers found the details for Tigger2a in our most recent 
> download of the RepBase library (release RELEASE 20061006, from this 
> month), reproduced here:
>
> ID   Tigger2a     repeatmasker; DNA;  ???;  434 BP.
> CC   Tigger2a DNA
> XX
> KW   DNA/MER2_type.
> XX
> CC   consensus - See RepBase for additional annotations.
> XX
> CC   RepeatMasker Annotations:
> CC        Type: DNA
> CC        SubType: MER2_type
> CC        Species: Primates
> CC        SearchStages: 40,50
> CC        BufferStages:
> CC        Description: (MER28)  14% div
> XX
> SQ   Sequence 434 BP; 115 A; 96 C; 80 G; 138 T; 5 other;
> cagttgaccc ttgaacaaca tgggtttgaa ctgcgtggrt ccacttatac gcggattttc   60
> ttccatctct gccaccctga gacagcaaga ccaacccctc ctcctcctca gcctactcaa   120
> cntgaagacg angaggatga agacctttat gatgatccac ttccacttaa tgaatagtaa   180
> atatattttc tcttccttat gattttctta ataacatttt cttttctcta gcttacttta   240
> ttgtaagaat acggtatata atacatataa catacaaaat atgtgttaat cgactgttta   300
> tgttatcggt aaggcttcca gtcaacagta ggctattagt agttaagttt tkggggagtc   360
> aaaagttata cgtggatttt tnactgcgcg gggggtcagc gcccctaacc cccgcgttgt   420
> tcaagggtca actg                                                     434
>
>
> Perhaps this annotation has only recently been removed from the 
> searchable online RepBase library.
>
> I hope this information helps.  If you have more questions, please do 
> not hesitate to contact us again.
>