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 ...
Possible consequences for splicing kinetics remain to be investigated in detail, but our analysis of RNA sequencing (RNA-seq) data indicated little or no effect of K1268R mutation on intron retention, and only very limited effects on the final splicing outcomes were observed in the absence of ...
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 ...
At the level of genomic DNA, the osteopetrosis mutation results in the deletion of 2781 bp of the SLC4A2 gene sequence, and thus the removal of roughly one-third of intron 1, the entire sequences of exon 2 and intron 2, and nearly half of exon 3. This has been confirmed by the suc...
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 ...