The total number of protein-coding genes in the human genome is not significantly higher than those in much simpler eukaryotes, despite a general increase in genome size proportionate to the organismal complexit
To confirm that ERLR was not a protein-coding transcript, three different software programs were applied to predict the coding potential of ERLR (Fig. S2A–C). The results revealed that ERLR does not have protein-coding potential. In addition, we searched the UCSC Genome Browser (Human Dec...
According to the chromosome location, lnc-EGFR is overlapped with the protein coding gene RNASE4. The specific primers and shRNAs for lnc-EGFR were designed in order to avoid the overlapping with RNASE4 (Supplementary Fig. 7). As expected, knockdown of lnc-EGFR had no apparent effect on exp...
Since recent studies have demonstrated that non-coding transcription is closely associated with CpG hypomethylation, we considered the possibility that transcription across the ThymoD region acts to recruit members of the Tet protein family (Benner et al., 2015). Hence, we examined DNA isolated from...
Long non-coding RNA Novel transcript discovery and annotation 1. Introduction Long non-coding RNAs (lncRNA) are known as non-protein coding transcripts longer than 200 nt. Although the information about their functions are so limited, studies revealed that they have several direct and indirect ...
Since decades it has been known that non-protein-coding RNAs have important cellular functions. Deep sequencing recently facilitated the discovery of thousands of novel transcripts, now classified as long noncoding RNAs (lncRNAs), in many vertebrate and invertebrate species. LncRNAs are involved in a...
In silico studies of available transcript sequence data have found that up to 24% of human protein coding loci also encode cis-NAT s [8, 9]. However, antisense transcripts tend to be poly(A) negative and nuclear localized [10]. If this is true, the abundance of NAT s (cis and trans...
基于人(GENCODE v25)和小鼠(GENCODE version M21)基因组的GENCODE注释,所有LINE1reads的基因组分布被指定为蛋白质编码protein coding、基因间intergenic、lncRNA、假基因pseudogene和非编码基因noncoding 。 13、从头重建含LINE1转录本De novo reconstruction of LINE1-containing transcripts 通过结合两种不同的从头转录...
We applied PLEK to human protein-coding transcripts with simulated indel sequencing errors to evaluate its robustness and compare its performance with that of CPC and CNCI. CPC is widely used to assess the protein-coding potential of a transcript based on alignment with a protein database [14,45...
Non-coding RNA in neurodegeneration When the Human Genome Project started in 1990, it was estimated that 30,000–40,000 protein coding genes would be found in the human genome [211]. When the project was completed in 2001, researchers were surprised to find far fewer protein coding genes tha...