![]() a reference sequence representing a protein-coding transcript must contain a complete CDS, otherwise it should be considered that the supporting evidence is insufficient to support the use of the transcript.the mechanism that identifies a complete record may be embedded in the sequence identifier or may be defined within the reference sequence record.The reference sequence database must provide a mechanism which allows simple and definitive identification of “complete” sequences only reference sequences considered to be “complete” (as defined in the bullet points below) are suitable for defining sequence variation.annotated records and downloadable formats such as fasta files the sequence identifier must be included in all representations of a reference sequence, i.e.3 is correct, NM_004006 is not correct (lacks the essential version number) In the context of these reference sequences, variant descriptions lacking a version number are not valid. RefSeq and Ensembl reference sequence identifiers use version numbers to distinguish between sequences.versioned reference sequence identifiers are required only when the reference sequence databases use versioning to distinguish between unique sequences.the structure and meaning of an identifier is determined by the source reference sequence database sequence identifiers are opaque ( note 1), i.e.a sequence identifier must only ever identify one reference sequence, and the sequence referred to by a sequence identifier may not be deleted or changed.within chromosomal reference sequences, and are not considered as undefined IUPAC codes for any nucleotide (N) or any amino acid (X) are permitted within a contiguous sequence, e.g.For example, a coding sequence will contain intron gaps when aligned to a genomic sequence Alignments between sequences may contain gaps. this requirement applies within a single sequence.reference sequence must be contiguous undefined sequence is not permissible.the sequence comprises a string of IUPAC codes that represents a nucleic acid or amino acid sequence using the conventional order (5’-to-3’ for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences) reference sequences must use conventional representation, i.e. ![]()
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