RT Journal
A1 Tajul-Arifin, Khairina
A1 Teasdale, Rohan
A1 Ravasi, Timothy
A1 Hume, David A.
A1 RIKEN GER Group
A1 GSL Members
A1 Mattick, John S.
T1 Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome
JF Genome Research 
JO Genome Research 
YR 2003 
FD June 01 
VO 13 
IS 6b 
SP 1416 
OP 1429 
DO 10.1101/gr.1015703 
UL http://genome.cshlp.org/content/13/6b/1416.abstract 
AB The chromodomain is 40–50 amino acids in length and is conserved in a  wide range of chromatic and regulatory proteins involved in chromatin  remodeling. Chromodomain-containing proteins can be classified into families  based on their broader characteristics, in particular the presence of other  types of domains, and which correlate with different subclasses of the  chromodomains themselves. Hidden Markov model (HMM)-generated profiles of  different subclasses of chromodomains were used here to identify sequences  encoding chromodomain-containing proteins in the mouse transcriptome and  genome. A total of 36 different loci encoding proteins containing  chromodomains, including 17 novel loci, were identified. Six of these loci  (including three apparent pseudogenes, a novel HP1 ortholog, and two novel  Msl-3 transcription factor-like proteins) are not present in the human genome,  whereas the human genome contains four loci (two CDY orthologs and two  apparent CDY pseudogenes) that are not present in mouse. A number of these  loci exhibit alternative splicing to produce different isoforms, including 43  novel variants, some of which lack the chromodomain. The likely functions of  these proteins are discussed in relation to the known functions of other  chromodomain-containing proteins within the same family.