6 votes
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How to find miRNA binding sites on a specific gene?

There are some tools for predicting the binding: TargetScan (based on seed match [primary], extra pairing, sequence context 1 — nucleotide composition around the site etc [secondary]) miRanda (based ...
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6 votes

Are non-coding RNAs introns?

A clarification on introns and exons. While it is true that introns are not a part of the mRNA as March Ho said, they are essentially transcribed. This may seem trivial but it is important to note. ...
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6 votes

Are non-coding RNAs introns?

While Ankur's answer is correct, it must be noted that not all non-coding RNAs are introns. An intron must be excised from an mRNA, which therefore means that any non-coding RNA that is not part of ...
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5 votes
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miRNA targets mRNAs

First you have to define what you really mean by miRNA-X targets mRNA-Y. If you mean direct targeting then there are assays to verify it. To verify if the miRNA can potentially target the mRNA ...
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3 votes
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Are microRNAs transcribed from the same DNA strand as their parent messenger RNAs?

The following bear on the question of the relationship of the transcription of microRNAs to that of the pre-mRNAs of protein-coding genes: Some microRNAs (termed ‘intergenic’) do not reside in a ...
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3 votes
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Which mRNAs enter P-bodies?

I don't really understand why mRNA processing doesn't simply occur in the cytoplasm. To be clear, P-bodies are in the cytoplasm (ie they are not separated by a membrane). There is also dynamic ...
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3 votes

Small non-coding RNA (sRNA) vs. micro RNA (miRNA)?

Small non-coding RNAs are NOT generally abbreviated as sRNA but as sncRNA, if anything. I say "if anything" because the "small" part is subjective and just a portmanteau descriptor. The straight ...
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2 votes

Are non-coding RNAs introns?

Yup - in a lot of cases the transcription of non-coding RNAs is from introns. Some of them are within genes (intragenic) and others are intergenic (between genes). In humans, a large number of both ...
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2 votes

Naming convention of miRNAs

Some general aspects about miRNA nomenclature in addition to canadianer's answer: mir refers to the pre-miRNA whereas miR ...
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2 votes

Difference between micro RNA and short-interfering RNA and CRISPR Cas 9 system?

The CRISPR Cas 9 system is used to introduce insertion or deletion in a genomic sequence not mRNA. https://www.addgene.org/CRISPR/guide/
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2 votes
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Small non-coding RNA (sRNA) vs. micro RNA (miRNA)?

miRNA are one member of the small non-coding RNA family. "Small non-coding" is a pretty broad term that encompasses microRNA and short interfering RNA, among other regulatory RNA species. The key ...
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2 votes

Can a miRNA be upregulated and downregulated in the same disease

Since diseases are frequently complex, it is not surprising to find specific genes (both miRNA coding genes or protein coding genes) being deferentially regulated when different studies of similar-...
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2 votes
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What is the difference between hsa-miR-33a and hsa-miR-33b?

They are paralogs i.e. they have high level of sequence homology. They may have the same seed sequence too (see this). The paralogs can have same targets if they have same seed sequence but it is not ...
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2 votes

Why does miRNA not get translated?

As you've noted, different RNA molecules are treated differently in (eukaryotic) cells (other common RNAs are tRNAs and rRNAs). Factors influencing this include the RNA sequence involving both ...
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1 vote

How to confirm secondary structure formation of Precursor miRNA on gel?

Disclaimer: Although I have attempted northern blots for miRNA, I haven't actually done the kind of experiment you are talking about. First of all you need controls. A negative control: a same ...
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1 vote

What is cognate miRNA?

The use of the word cognate in molecular biology reflects adjectival definition 2 from Lexico: 2 formal Related; connected. ‘cognate subjects such as physics and chemistry’ The example given shows ...
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1 vote
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Why are there two mature sequences of microRNAs in miRBase entries?

I am not sure whether it is made clear in the Wikipedia article on microRNAs, but, yes, there are two possible mature mir species that can be generated from the stem-loop precursor — one from each ...
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1 vote

Do all microRNA isoforms need to be known and sequenced to obtain microRNA expression?

I had worked on a similar problem and I am telling my experience. First, you have to consider the fact that a mature miRNA can arise from multiple genomic locations i.e. many pre-miRNAs can give rise ...
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1 vote

miRNA targets mRNAs

mRNA targeting mechanism is highly specific and depends on various factors. the target mRNA and miRNA complex is highly conserved even from an evolutionary point of view.There are many in-vitro ...
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1 vote
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Naming convention of miRNAs

let-7 is a miRNA family (let stands for lethal) and, in fact, was one of the first to be discovered (in Caenorhabditis elegans). let-7a is but one of many members of the family, with orthologs in many ...
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1 vote

Relative microRNA comparison from from TCGA data?

Small RNA sequencing is good for a preliminary screen because as with most high throughput experiments, the sample size is less and therefore inter-sample comparisons may not be accurate. For miRNA ...
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1 vote

Relative microRNA comparison from from TCGA data?

I would be very careful in making such a claim from sequencing data. There are well known biases in sequencing due to things like GC composition and hexamer composition. Because of this, it's possible ...
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1 vote

How to find miRNA binding sites on a specific gene?

I would thoroughly check the literature on the UTR you are interested in, a lot of this has already been done for many genomic regions since nextgen seq began. You will want to first off use ...
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1 vote

Periods of Heavy Speciation

My guess (as your question need heavy editing!!) would be MiRdup. MiRdup Goals: Validation of pre-miRNAs predictions Prediction of mature miRNA Abstract: MicroRNAs (miRNAs) are ...
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1 vote
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Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?

There is no hard and fast rule for how many nucleotides you have to select. If your miRNA is ~20nt and you take 70nt from both sides (average length of hairpins is ~84nt in humans), your total length ...
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Steps to confirm if predicted miRNA is good or bad

There won't be any duplicates in miRBase (for a given organism). Choose the taxon nearest to your organism if you are doing homology based discovery. If you want to take all/many organisms then you ...
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1 vote
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mFOLD prediction result interpretation

The green region will definitely not make an miRNA: It is not a part of a stem loop. See typical miRNA structures from miRbase. EDIT Bulges can sometimes determine which strand is chosen as mature ...
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