Please, read the following papers for the gene, SECIS and SNP annotation procedures:

Harrow J, Frankish, A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al.
GENCODE: the reference human genome annotation for The ENCODE Project
Genome Res., 22, 1760-1774 (2012)

Mariotti M, Guigó R
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
Bioinformatics, 26, 2656-2663 (2010)

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M et al.
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Nat. Genet., 41, 491-498 (2011)