alphagenome.data.gene_annotation.TranscriptType#
- class alphagenome.data.gene_annotation.TranscriptType(value)[source]#
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).
Attributes#
Table
- TranscriptType.IG_C_GENE = 'IG_C_gene'#
- TranscriptType.IG_C_PSEUDOGENE = 'IG_C_pseudogene'#
- TranscriptType.IG_D_GENE = 'IG_D_gene'#
- TranscriptType.IG_J_GENE = 'IG_J_gene'#
- TranscriptType.IG_J_PSEUDOGENE = 'IG_J_pseudogene'#
- TranscriptType.IG_V_GENE = 'IG_V_gene'#
- TranscriptType.IG_V_PSEUDOGENE = 'IG_V_pseudogene'#
- TranscriptType.IG_PSEUDOGENE = 'IG_pseudogene'#
- TranscriptType.MT_RRNA = 'Mt_rRNA'#
- TranscriptType.MT_TRNA = 'Mt_tRNA'#
- TranscriptType.TEC = 'TEC'#
- TranscriptType.TR_C_GENE = 'TR_C_gene'#
- TranscriptType.TR_D_GENE = 'TR_D_gene'#
- TranscriptType.TR_J_GENE = 'TR_J_gene'#
- TranscriptType.TR_J_PSEUDOGENE = 'TR_J_pseudogene'#
- TranscriptType.TR_V_GENE = 'TR_V_gene'#
- TranscriptType.TR_V_PSEUDOGENE = 'TR_V_pseudogene'#
- TranscriptType.ARTIFACT = 'artifact'#
- TranscriptType.LNCRNA = 'lncRNA'#
- TranscriptType.MIRNA = 'miRNA'#
- TranscriptType.MISC_RNA = 'misc_RNA'#
- TranscriptType.NON_STOP_DECAY = 'non_stop_decay'#
- TranscriptType.NONSENSE_MEDIATED_DECAY = 'nonsense_mediated_decay'#
- TranscriptType.PROCESSED_PSEUDOGENE = 'processed_pseudogene'#
- TranscriptType.PROCESSED_TRANSCRIPT = 'processed_transcript'#
- TranscriptType.PROTEIN_CODING = 'protein_coding'#
- TranscriptType.PROTEIN_CODING_CDS_NOT_DEFINED = 'protein_coding_CDS_not_defined'#
- TranscriptType.PROTEIN_CODING_LOF = 'protein_coding_LoF'#
- TranscriptType.RRNA = 'rRNA'#
- TranscriptType.RRNA_PSEUDOGENE = 'rRNA_pseudogene'#
- TranscriptType.RETAINED_INTRON = 'retained_intron'#
- TranscriptType.RIBOZYME = 'ribozyme'#
- TranscriptType.SRNA = 'sRNA'#
- TranscriptType.SCRNA = 'scRNA'#
- TranscriptType.SCARNA = 'scaRNA'#
- TranscriptType.SNRNA = 'snRNA'#
- TranscriptType.SNORNA = 'snoRNA'#
- TranscriptType.TRANSCRIBED_PROCESSED_PSEUDOGENE = 'transcribed_processed_pseudogene'#
- TranscriptType.TRANSCRIBED_UNITARY_PSEUDOGENE = 'transcribed_unitary_pseudogene'#
- TranscriptType.TRANSCRIBED_UNPROCESSED_PSEUDOGENE = 'transcribed_unprocessed_pseudogene'#
- TranscriptType.TRANSLATED_PROCESSED_PSEUDOGENE = 'translated_processed_pseudogene'#
- TranscriptType.UNITARY_PSEUDOGENE = 'unitary_pseudogene'#
- TranscriptType.UNPROCESSED_PSEUDOGENE = 'unprocessed_pseudogene'#
- TranscriptType.VAULT_RNA = 'vault_RNA'#