Autonomous underwater vehicles (AUVs) are sophisticated robotic platforms crucial for a wide range of applications. The accuracy of AUV navigation systems is critical to their success. Inertial sensors and Doppler velocity logs (DVL) fusion is a promising solution for long-range underwater navigation. However, the effectiveness of this fusion depends heavily on an accurate alignment between the inertial sensors and the DVL. While current alignment methods show promise, there remains significant room for improvement in terms of accuracy, convergence time, and alignment trajectory efficiency. In this research we propose an end-to-end deep learning framework for the alignment process. By leveraging deep-learning capabilities, such as noise reduction and capture of nonlinearities in the data, we show using simulative data, that our proposed approach enhances both alignment accuracy and reduces convergence time beyond current model-based methods.