Subject:
summary of pseudogene call on Thurs. 6-Oct at 10:30 AM EDT
Date:
Thu, 06 Oct 2005 23:41:49 -0400

Hi,

here is a brief summary of relevant points from today's call.

cheers, amrK

==

1. Most important, Robert will give Alex ASAP a list of ~130 pseudogenes with
their DNA alignments to parent genes. Alex and Tom will use RT-PCR and RACE to
find transcription evidence for these pseudogenes.

2. We implement the qualified union approach with consistent boundary proposal
and aim to get a draft concensus set done before the 15th. I'd suggest next Wed.
as the deadline. I propose that Adam and Deyou work together to implement the
below steps.

a. We will take a union of all the current ENCODE pseudogenes from 4 groups --
Yale (167), Havana (165), GIS (46), UCSC (146).

b. We will remove pseudogenes overlapping with current GENCODE exons or gene loci.

c. We will identify a parent protein for each of the remaining pseudogenes using
the exact UniProt set that HAVANA uses. Pseudogenes without a matching protein
will not be excluded. (Havana should send a link to this to the whole group.)

d. We will align each pseudogene to its parent to define boundary of each
pseudogene.

3. We will present this list of consensus pseudogenes in the UCSC browser. A
synched copy of this will also be available from pseudogene.org/ENCODE and
Havana/VEGA.

4. I think we should plan on a call next week to go over the UCSC and Havana ppt
that we didn't have time to do today. We should only have this call AFTER we
have completed our initial union. I think we should aim for Thurs. or Fri. for
the call. How is Thurs. at 11 AM?