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Transcript models

An effect may carry a MutantTranscript describing edits, retained reference segments, or an observed RNA structure. It can contain cDNA and protein sequence, but it may also be partial or have no resolved sequence.

You usually want the effect's mutant_protein_sequence; a transcript model is useful when you also need the RNA structure or its provenance. Not every effect has a model, even when a predicted protein is available.

Sequence access

Given an annotated effect:

protein = effect.mutant_protein_sequence
model = effect.mutant_transcript
cdna = model.cdna_sequence if model is not None else None
evidence = model.evidence if model is not None else None

None means unavailable. It does not establish an unchanged protein, an absent transcript, or a harmless variant.

Selenocysteine

Ensembl marks selenocysteine (Sec) as U in the reference protein, encoded by an in-frame UGA. UGA is decoded as Sec only with a SECIS element in the same mRNA's 3′ UTR, whose position isn't annotated. Predicted proteins read an annotated Sec codon as U when the model still maps it (no edit touches it) and keeps some of a selenoprotein's 3′ UTR. Where no selenoprotein 3′ UTR remains, for example a fusion downstream of Sec, UGA is read as a stop. A sequence without reference coordinates, such as an imported RNA assembly, is translated literally. A partly kept 3′ UTR still gets the Sec reading; the SV change flags report such cases as unresolved.

Partial structures

A model with reference segments is not necessarily a complete mutant RNA. For example, a breakend can retain only a transcript's local 5′ prefix or 3′ suffix. That model has evidence["sequence_status"] = "retained_reference_fragment", while full cDNA and protein remain unknown. Concatenating its segments does not reconstruct the missing partner or establish the full allele.

Likewise, a sequence supplied by an RNA assembler may be only a junction fragment. Keep its completeness and source information with the sequence. The RNA import guide explains how observed structures and sequence-predicted proteins are represented; neither alone proves translation.

Object Contents
MutationEffect A predicted consequence or an unresolved result
MutantTranscript Edits or transcript structure, provenance, and optional sequences
MultiOutcomeEffect Several candidate effects, each with its own consequence and evidence

The API reference lists model fields and construction helpers. The experimental transcript-model annotator uses additional baseline and mutant product wrappers; see its result format.