SINES and LINES in dog

[Arumilli, Meharji]

Dear all,

I have downloaded the Repeats for dog genome from the UCSC table browser
(http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=494847877_EkxQdv7amBBbkmbtoG3FAABmfsNp&clade=mammal&org=Dog&db=canFam3&hgta_group=varRep&hgta_track=rmsk&hgta_table=0&hgta_regionType=genome&position=chr14%3A8114295-8120760&hgta_outputType=selectedFields&hgta_outFileName=canis_familiaris.gaps)

I am interested in SINE/LINE element and in the repClass it gives the
info whether it belongs to SINE or LINE. However, in the repName column
there are different names for these elements.

For instance, to list a few names in the LINE class:

L1_Canid
L1_Canid_
L1_Canid2
L1_Canis1
L1_Canis2
L1_Carn1

Similary, a few names in the SINE class:

SINEC_a1
SINEC_a2
SINEC_b1
SINEC_b2
SINEC_c1
SINEC_c2
SINEC_Cf
SINEC_Cf2
SINEC_Cf3

Does all these names correspond to the SINEs/LINEs in the dog genome?
Is there some naming convention to filter for dog specific repeats?


Br

Mehar

[Luvina Guruvadoo]

Hello Mehar,

Thank you for your question. One of our engineer notes that you can pick up the repbase library from:

http://www.girinst.org/

file: RepeatMaskerLib.embl

This file contains species indication and repeat identifier as seen from this grep: egrep "RepbaseID:|Species:" RepeatMaskerLib.embl

The version we have been using in recent times is from 31 Jan 2014 '20140131'.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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