I would like to know if there is any difference between the genome build fasta files from UCSC and Gencode/Ensembl ? For example, is there any difference between the GRCh38/hg38 of UCSC to Gencode/Ensembl and similarly for mm10/GRCh38 of UCSC and Gencode/Ensembl ?
If not, then why there is a difference in genomic coordinates of these genes ? For example why Mecp2 coordinates in UCSC for GRCh38/hg38 is chrX:154,021,813-154,097,731 and for Ensembl Chromosome X: 154,021,573-154,137,103
Can I use the fasta file downloaded from NCBI/UCSC and annotation file downloaded from Gencode for alignment and other bioinformatics downstream purposes ?