1DBTSS (DataBase of human Transcriptional Start Sites) DBTSS (Wakaguriet al., 2008) is a database which contains precise positional information for TSSs of eukaryotic mRNAs. Using the newly developed oligo-capping method, full-length cDNAs were obtained and used to extend existing cDNA libraries...
YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants th... J Mcmillan,Z Lu,JS Rodriguez,... - Oxford Academic 被引量: 0发表...
CPM, counts per million mapped reads; TSS, transcription start site; TES, transcription end site. Data represent the average of three replicates. f, DPC residual ratios represent the proportions of sequence coverage of each gene in cells recovered for 4 h divided by that of cells not ...
we have reanalyzed published CAGE data of RNA start base distribution by pooling CAGE Transcription Start Sites (CTSSs) with at least 1 tag per million (TPM) across 12 stages in zebrafish embryo development3(Fig.1a). The majority of CTSSs (71.6%) have canonical (Y−1R+1) start sites ...
CISMAPPER also predicts which TF binding sites regulate a given gene more accurately than using genomic distance. Unlike distance-based methods, CISMAPPER can predict which transcription start site of a gene is regulated by a particular binding site of the TF. 展开 ...
start and stop codons. This approach yielded 221 TSS, associated with 71 new and 150 alternative translational units (Additional file2: Table S3). To increase the probability of annotating only genuine open reading frames (ORFs), we searched the NCBI nonredundant protein database for orthologs ...
ecRNAs begin transcription upstream of the transcription start site (TSS) and terminate downstream of the TES of the gene they regulate. Cebpa and Fos have regulatory ecRNAs, so we compared their post-TES sense transcript levels to Hdac2 and identified post-TES signal for all genes. Hdac2 ...
The scale denotes nucleotides, and an arrow at the +1 nucleotide represents the transcription start site. Information used to generate this image was taken from the EcoCyc database [52] and references therein. (b) The ability of the NarL proteins to repress frdA-lacZ expression, or (c) to...
(b) experiments. Position 1 corresponds to the start position of the ATAC/DNase-seq read. The size of the motifs is reflected by the structural protein contacts of Tn5 and DNase-I (Protein Data Bank entries 1MM8 and 2DNJ).cTn5 inserts adapters in both DNA ends. Moreover, DNA is ...
Two thousand bp upstream of the transcriptional start site of each SsAP2/ERF gene was selected to inspect potential CREs. They were submitted to the PlantCARE website (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/). Transcriptome data source and bioinformatic analysis Sugarcane tissue...