Condor

RNA Type: CNE

Overview: Condor is a database of Conserved Non-coding Elements (CNE) extracted from multiple alignments of orthologous genomic regions of fugu and mammalian genomes. There are two types of information stored in the database: conservation information in vertebrates, obtained from the alignments, and information related to experimentally validated CNEs acting as putative promoter enhancers in different samples/tissues of zebrafish embryos.

Search Methods:

• Similarity: search sequences against the Condor CNEs or genomic assemblies used in multiple alignment. The BLAST program is used in both searches.
• Keyword: search by CNE accession code, gene name, SPTR accession, Ensembl accession, GO accession etc.
• TAG: search by gene name or CNEs in gene expression data in several tissues (i.e., brain, eye, muscle, blood, etc.) and stages (i.e., 24-30 hfp). The user can specify the minimum percentage of in at least N% of expressing embryos.

Source: Experiments (in vivo assay - zebrafish embryo), Fugu Information Network, Ensembl and In house analysis (BLAST, Repeat-Masker, EntropyRep, MLAGAN/SLAGAN and VISTA programs).

Information Source: Experimental, In silico annotation.

Information Content: Alignment, Annotation, Cis-regulatory elements, Conserved Non-coding Elements, Developmentalregulators, Embryos (zebrafish), Expression, Organ, Orthologs, Sequence, Stage, Tissue.

Reference: Woolfe et al., 2007

PubmedID: 17760977.

Year: 2007

Multiple search: Yes

Download: BED, FASTA, Other.

Genomic Overview: No

Organism: Homo sapiens (Human), Rattus norvegicus (Norway Rat), Canis familiaris (Dog), Mus musculus (House Mouse), Danio rerio (Zebrafish), Takifugu rubripes (Fugu).

Url: http://condor.nimr.mrc.ac.uk/