Synonymous gene regulation (identified by shared tissue and timepoint specificities) is established through genomic elements that contain a specific cluster of transcription factor binding sites (TFBS). SynoR performs vertebrate genome scans for evolutionary conserved clusters of TFBS in a predefined configuration to identify synonymous regulatory elements (SREs). SynoR searches for SREs by utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Multiple-species conservation layers allow the use of differential conservation filters in the search for SREs and SynoR results provide an extensive annotation of identified genes that contain detected REs. Gene Ontology classifiers are utilized to perform functional classification of the identified genes, and integrated GNF Expression Atlas data permits on-the-fly analysis of tissue-specificities of predicted SREs. SynoR is located at //synor.dcode.org/.