TranscriptType

class alphagenome.data.gene_annotation.TranscriptType(value)

Valid Transcript types available in the GENCODE GTF.

IG_C_GENE

Immunoglobulin constant region gene.

IG_C_PSEUDOGENE

Inactivated immunoglobulin constant pseudogene.

IG_D_GENE

Immunoglobulin diversity region gene.

IG_J_GENE

Immunoglobulin joining region gene.

IG_J_PSEUDOGENE

Inactivated immunoglobulin joining pseudogene.

IG_V_GENE

Immunoglobulin variable region gene.

IG_V_PSEUDOGENE

Inactivated immunoglobulin variable pseudogene.

IG_PSEUDOGENE

General inactivated immunoglobulin pseudogene.

MT_RRNA

Mitochondrial ribosomal RNA.

MT_TRNA

Mitochondrial transfer RNA.

TEC

To be experimentally confirmed transcript.

TR_C_GENE

T-cell receptor constant region gene.

TR_D_GENE

T-cell receptor diversity region gene.

TR_J_GENE

T-cell receptor joining region gene.

TR_J_PSEUDOGENE

Inactivated T-cell receptor joining pseudogene.

TR_V_GENE

T-cell receptor variable region gene.

TR_V_PSEUDOGENE

Inactivated T-cell receptor variable pseudogene.

ARTIFACT

Annotation or sequencing artifact transcript.

LNCRNA

Long non-coding RNA transcript.

MIRNA

MicroRNA transcript.

MISC_RNA

Miscellaneous non-coding RNA transcript.

NON_STOP_DECAY

Transcript lacking an in-frame stop codon.

NONSENSE_MEDIATED_DECAY

Transcript targeted for nonsense-mediated decay.

PROCESSED_PSEUDOGENE

Pseudogene derived from reverse-transcribed mRNA.

PROCESSED_TRANSCRIPT

Non-coding spliced transcript without an ORF.

PROTEIN_CODING

Transcript with an open reading frame encoding a protein.

PROTEIN_CODING_CDS_NOT_DEFINED

Protein-coding gene isoform without a CDS.

PROTEIN_CODING_LOF

Protein-coding transcript with loss-of-function allele.

RRNA

Ribosomal RNA transcript.

RRNA_PSEUDOGENE

Ribosomal RNA pseudogene.

RETAINED_INTRON

Alternative isoform retaining at least one intron.

RIBOZYME

Catalytic RNA transcript.

SRNA

Small bacterial-type non-coding RNA.

SCRNA

Small cytoplasmic RNA.

SCARNA

Small Cajal body-specific RNA.

SNRNA

Small nuclear RNA.

SNORNA

Small non-coding RNA guiding chemical RNA modifications (snoRNA).

TRANSCRIBED_PROCESSED_PSEUDOGENE

Transcribed processed pseudogene.

TRANSCRIBED_UNITARY_PSEUDOGENE

Transcribed unitary pseudogene.

TRANSCRIBED_UNPROCESSED_PSEUDOGENE

Transcribed unprocessed pseudogene.

TRANSLATED_PROCESSED_PSEUDOGENE

Translated processed pseudogene.

UNITARY_PSEUDOGENE

Species-specific pseudogene without functional parent.

UNPROCESSED_PSEUDOGENE

Duplicated pseudogene retaining exon-intron layout.

VAULT_RNA

Short non-coding RNA component of vault complexes (vRNA).