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Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression. Overall design: 19 tissues and primary cell types were examined."],"tag":["xref:PubMed:22763441"],"repository":["ENA"],"description_synonyms":["ahl4, MUTYH-Associated Polyposis, methionine aminopeptidase activity, Laboratory, Mus domesticus, MYH-associated polyposis, mouse, autosomal recessive familial adenomatous polyposis, Maps, RNA-seq., 2610511A05Rik, House Mouse, BB234005, House, Mus, Cis, CIS, G18, Mus musculus domesticus, 2, Whole Transcriptome Shotgun Sequencing, Mice, familial adenomatous polyposis, MAP, peptidase M activity, autosomal recessive, adenomas, Mus musculus, RUTBC3, rabGAPLP, CIS-1, L-methionine aminopeptidase activity, Genomes, Swiss, mice, familial adenomatous polyposis 2, Swiss Mouse, RabGAP-5, 9030605P22Rik, House Mice, Swiss Mice, whole genome, MYH-Associated Polyposis, RABGAP5, domesticus, Laboratory Mice, autosomal recessive multiple colorectal adenomas, SOCS, RUSC3, multiple colorectal, Protein G18, MAP syndrome, Mouse, house mouse, Suppressor of cytokine signaling, Laboratory Mouse, BACTS2, FAP2, colorectal adenomatous polyposis"],"name_synonyms":["Mus musculus, Laboratory Mice., House, Mus, Laboratory, Swiss, Mus domesticus, mouse, Mus musculus domesticus, Swiss Mouse, mouse <Mus musculus>, Mouse, House Mice, Swiss Mice, house mouse, Mice, Laboratory Mouse, House Mouse, mice C57BL/6xCBA/CaJ hybrid, domesticus, Mus muscaris"],"additional_accession":[]},"is_claimable":false,"name":"Mus musculus","description":"A draft map of cis-regulatory sequences in the mouse genome [RNA-Seq]","dates":{"last_updated":"2025-09-24","first_public":"2013-05-31"},"accession":"PRJNA142823","cross_references":{"GEO":["GSE29278"],"taxon":["10090"],"PubMed":["22763441"]}}