Genomic loci are defined bifunctional when they can be considered both coding (orange) and non-coding (blue), because they express both an mRNA and a ncRNA, through one of the following mechanisms.aThe ncRNA is
Recent reports show that long non-coding RNAs (lncRNAs) have inefficient splicing and fewer alternative splice variants than mRNAs. Here, we have explored the efficiency of lncRNAs and mRNAs in producing various splice variants, given the number of exons in humans and mice. Intriguingly, lncRNAs ...
Genome and RNA-Seq file from the same species (see figure 3); this approach is suitable for short read RNA-Seq libraries with a good coverage of the transcriptome, important: this approach requires that each intron is covered by many alignments, i.e. it does not work with assembled transcr...
--alignSJoverhangMin 8; --alignSJDBoverhangMin 10; --outFilterMismatchNmax 999; --outFilterMismatchNoverReadLmax 0.04; --alignSJstitchMismatchNmax 5 -1 5 5; --outSAMattrRGline ID:GRPundef; --alignIntronMin 20; --alignIntronMax 1000000; --alignMatesGapMax 1000000 for unique alignments. To...
Noncoding exon 2 and coding exon 3 of the FKRP gene are depicted by open boxes. Probe PB3/4 identifies positive embryonic stem cell clones in Southern blots of genomic DNA digested with EcoRV. Dashed lines represent genomic sequence not included in the targeting vector. The LA and SA are ...
domestica IGF2 gene was input into the bioinformatics program MAR-Wiz [23], a region within the first intron just downstream of the 5' noncoding exon was predicted to be a Matrix Attachment Region (92% average strength) (Figure 2A). FISH using a 5 kilobase probe containing the predicted ...
We found that sponge genes coding for Group I Nme protein are intron-rich. Furthermore, we discovered that the sponge NmeGp1Sd protein has a similar level of kinase activity as its human homolog Nme1, does not cleave negatively supercoiled DNA and shows nonspecific DNA-binding activity. The ...
However, probes targeting C9ORF72 intron 7, which detect V2 and V3 pre-mRNA, exhibited a statistically significant reduction of this RNA sequence in C9ORF72 ALS compared to control and non-C9ORF72 ALS tissue, suggesting that the prespliced levels of C9ORF72 V2 and V3 RNA are also reduced...
intron [43]. They both also methylate pre-mRNAs of SAM synthetases to affect SAM homeostasis with distinct molecular features. Mammalian METTL16 installs m6A on the UACm6AGAGAA motifs at 3′ UTR of SAM synthetasesMAT2Apre-mRNA, which leads to intron retention/decay of the RNA and affects ...
In previous work we and others demonstrated robust allele-specific expression ofGabra2(Hawkins et al.2019,2016; Mulligan et al.2019,2012; Yu et al.2020). Also, we established that unusually low GABRA2 protein expression is caused by a non-coding single nucleotide deletion in the C57BL/6J ...