CRISPR sgRNA design:
http://crispr.mit.edu/

RNA structure:

NUPACK can be downloaded here.

mFOLD can be accessed here.

 

KineFold (for animating RNA folding) can be accessed here.

Finding Post-translational Modifications:

PhosphoSitePlus is very comprehensive and has a good search function to allow you to find sites of phosphorylation, ubiquitination, acetylation, and other modifications in proteins of interest.

Phosidia seem redundant with PhosphositePlus and only tabulates phosphorylation, ubiquitination, and glycosylation, but it is worth looking at just in case.

Repositories of embryo/animal-wide gene expression patterns:

BioGPS is a useful database of gene expression patterns in human, mouse, and rat tissues and cell lines

Allen Brain Atlas: a molecular map showing where all genes are expressed in all regions of the brain

Emage

The Gene expression database from Jackson Labs allows you to search for gene expression by gene, tissue, Affymetrix gene identifier, and several other parameters.  Click "Expression" from this page.

Mouse atlas of gene expression