A shot in the dark, the conservation track tells you how the specific gene segment or stretch of DNA was conserved among the different species in questions. So, if galgal3 has a conservation track, you should simple be able to liftOver that and use it for your purposes, until new homology/convervation analysis is done.

http://moma.ki.au.dk/genome-mirror/cgi-bin/hgTrackUi?db=anoCar2&g=cons7way

EDIT

Liftover of conservation track (mutli7z) from galgal3 to galgal4

multi7z This track shows a measure of evolutionary conservation in 7 vertebrates, including bird, mammalian, amphibian, and fish species, based on a phylogenetic hidden Markov model, phastCons (Siepel et al., 2005). Multiz alignments of the following assemblies were used to generate this track:

chicken (May 2006 (WUGSC 2.1/galGal3), galGal3) human (Mar 2006, hg18) mouse (Feb 2006, mm8) rat (Nov 2004, rn4) opossum (Jan 2006, monDom4) X. tropicalis (Aug 2005, xenTro2) zebrafish (Mar 2006, danRer4)

Download the multi7z track from galgal3 ucscftp

http://hgdownload.cse.ucsc.edu/goldenPath/galGal3/database/multiz7way.txt.gz

Gunzip and convert it to bed,

gunzip -c multiz7way.txt.gz | cut -f2-7 > multiz7way.bed

Download the liftOver chain file,

http://hgdownload.cse.ucsc.edu/goldenPath/galGal3/liftOver/galGal3ToGalGal4.over.chain.gz

Download the liftOver utility for your system architecture, http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver

Then execute,

liftOver multiz7way.bed galGal3ToGalGal4.over.chain.gz multiz7way_mapped.bed multiz7way_unmapped.bed

multiz7way_mapped.bed is your file, convert it to bedGraph (coverage file) or bam/wig/bigwig, whatever you like and upload as a custom track to ucsc.

Please confirm the efficacy of this answer, before using it in downstream research.

Cheers

Have you tried looking at your data in Ensembl? Galgal4 is used in our 21 amniota vertebrates PECAN analysis, our 4 sauropsids EPO analysis and our 7 sauropsids EPO_LOW_COVERAGE analysis. You can attach your ChIP-Seq data as the original BAM files.