In OpenGL, is there a way to blend based on a separate channel's value in the shader?

In OpenGL (not ES), is there a universal way to blend based a texture while drawing based on another texture or variable's value? On OpenGLES, I know that I can do custom blending on some platforms via extensions like GL_EXT_shader_framebuffer_fetch. The reason I ask, is that I have a special texture where the forth channel is not alpha, and I need to be able to blend it on a separate alpha which is available on a different map.