miRNA - targets (Jan/31/2011 )
The differences between the miRNA with different letters example:
miRNA133
miRNA 133a
miRNA 133b
miRNA 133*
Do all these miRNA regulate the same/similar targets?
When one of these is increased in any condition - will the others also be altered?
Thanks
133a and 133b are isoforms of 133. These isoforms differ by 1 or 2 nucleotides only. Its unknown whether isoforms act on the same things or are targeted by the same factors. My guess would be that they more or less do the same thing but maybe are activated or regulated differently due to these slight differences, but that's just my guess of course.
133* --> the * indicates that its the less predominant arm of the pre-cursor microRNA (although I have read lots of papers that indicate that these * miRNA are just as important as the non * and that cell type and developmental stage may play a role in which "arm" is predominant)
An alternative to * versus non-* is the use of -5p and -3p, where each suffix represent one arm of the precursor miRNA.
Here's a link with a brief explanation of miRNA nomenclature
http://www.mirbase.org/help/nomenclature.shtml
biotechgirl on Mon Jan 31 18:57:51 2011 said:
133a and 133b are isoforms of 133. These isoforms differ by 1 or 2 nucleotides only. Its unknown whether isoforms act on the same things or are targeted by the same factors. My guess would be that they more or less do the same thing but maybe are activated or regulated differently due to these slight differences, but that's just my guess of course.
133* --> the * indicates that its the less predominant arm of the pre-cursor microRNA (although I have read lots of papers that indicate that these * miRNA are just as important as the non * and that cell type and developmental stage may play a role in which "arm" is predominant)
An alternative to * versus non-* is the use of -5p and -3p, where each suffix represent one arm of the precursor miRNA.
Here's a link with a brief explanation of miRNA nomenclature
http://www.mirbase.org/help/nomenclature.shtml
Thanks. What are the best sites/databases to determine mouse miRNA targets.
JJA on Mon Jan 31 19:44:49 2011 said:
biotechgirl on Mon Jan 31 18:57:51 2011 said:
133a and 133b are isoforms of 133. These isoforms differ by 1 or 2 nucleotides only. Its unknown whether isoforms act on the same things or are targeted by the same factors. My guess would be that they more or less do the same thing but maybe are activated or regulated differently due to these slight differences, but that's just my guess of course.
133* --> the * indicates that its the less predominant arm of the pre-cursor microRNA (although I have read lots of papers that indicate that these * miRNA are just as important as the non * and that cell type and developmental stage may play a role in which "arm" is predominant)
An alternative to * versus non-* is the use of -5p and -3p, where each suffix represent one arm of the precursor miRNA.
Here's a link with a brief explanation of miRNA nomenclature
http://www.mirbase.org/help/nomenclature.shtml
Thanks. What are the best sites/databases to determine mouse miRNA targets.
There are a bunch of online target prediction programs. They all use different methods to predict potential miRNA interactions. My favorite are TargetScan and Diane Lab. Target Scan is good because it takes into account conservation of sequences across species. Diane Lab is nice because it tries to pool predictions from different sources like Target Scan, PicTar, etc. There are also some others like StarBase that give Seq-ChiP data.
There are very few miRNA out of the total miRNA who's targets have been determined experimentally. A good place to start is the predictor websites I listed above and then check out papers online. Good luck!