Colored point cloud becomes a fundamental representation in the realm of 3D vision. Effective Point Cloud Compression (PCC) is urgently needed due to huge amount of data. In this paper, we propose an end-to-end Deep Joint Geometry and Attribute point cloud Compression (Deep-JGAC) framework for dense colored point clouds, which exploits the correlation between the geometry and attribute for high compression efficiency. Firstly, we propose a flexible Deep-JGAC framework, where the geometry and attribute sub-encoders are compatible to either learning or non-learning based geometry and attribute encoders. Secondly, we propose an attribute-assisted deep geometry encoder that enhances the geometry latent representation with the help of attribute, where the geometry decoding remains unchanged. Moreover, Attribute Information Fusion Module (AIFM) is proposed to fuse attribute information in geometry coding. Thirdly, to solve the mismatch between the point cloud geometry and attribute caused by the geometry compression distortion, we present an optimized re-colorization module to attach the attribute to the geometrically distorted point cloud for attribute coding. It enhances the colorization and lowers the computational complexity. Extensive experimental results demonstrate that in terms of the geometry quality metric D1-PSNR, the proposed Deep-JGAC achieves an average of 82.96%, 36.46%, 41.72%, and 31.16% bit-rate reductions as compared to the state-of-the-art G-PCC, V-PCC, GRASP, and PCGCv2, respectively. In terms of perceptual joint quality metric MS-GraphSIM, the proposed Deep-JGAC achieves an average of 48.72%, 14.67%, and 57.14% bit-rate reductions compared to the G-PCC, V-PCC, and IT-DL-PCC, respectively. The encoding/decoding time costs are also reduced by 94.29%/24.70%, and 96.75%/91.02% on average as compared with the V-PCC and IT-DL-PCC.