(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Eukaryota: NE > Opisthokonta: NE > Metazoa: NE > Eumetazoa: NE > Bilateria: NE > Protostomia: NE > Ecdysozoa: NE > Nematoda: NE > Chromadorea: NE > Rhabditida: NE > Rhabditoidea: NE > Rhabditidae: NE > Peloderinae: NE > Caenorhabditis: NE > Caenorhabditis brenneri: NE
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MGGFLSDLKPEINSEILYSSCGPIHGNVYKHEDKIVEGYLGIPFAEPPER FQKPIEANIWNDVKQCTTYGPGCPQSGIFDQMRDQLGLVFDEHKCLSLNV FVPQWKRDEVPPGFPVIVNIFGGGFEMGTSAAYDDFSISGTLPLKDVIVV TINYRVGAYGFFTTGDDVCHGNFALWDQTLALKWIQKHIASFGGNPKNVT VVGCSAGGVCADLLTLSTHSRDLFQKCISMSGSADCEMACRSSENQAKIF REFAMENGCYKNAVPDPVYTRIGDNIDFSASKLFGPDVVDDSEDVLKTLN DSYLQGIEQSNTVSVRKRFIEFLGDAVFNDGILKSVQSAAKSGNDVYFYS FDFCNPDGYGPLGEMLDFKASSHGNDFRYIFGVGGYEKFVPNDQELEVME MMITMFSNFAKYGNPNGVESNGIWEKYTLSSPGTYFKIDHPTSEMKNGFL NDRLAKIKAIERKIINF
To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced approximately 0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide.
