transcripts

Data license: ODbL · Data source: Larue & Roy, 2023 · About: Minor Intron Database (WtMTA)

id

INTEGER (primary key), unique identifier for each transcript

taxonomy_id

INTEGER (foreign key referencing genomes(taxonomy_id)), NCBI taxonomy identifier for species

transcript_id

TEXT, annotated identifier for the transcript

gene_id

TEXT, annotated identifier for the associated gene

chromosome

TEXT, chromosome (or contig) where the transcript is located

strand

TEXT, DNA strand of the transcript (+ or -)

start

INTEGER, start position of the transcript in the genome (1-based, inclusive)

end

INTEGER, end position of the transcript in the genome (1-based, inclusive)

coding_length

INTEGER, length of the coding sequence in base pairs

introns_per_kbp_cds

REAL, number of introns per kilobase coding sequence

proportion_minor_introns

REAL, proportion of minor introns in the transcript

n_introns

INTEGER, total number of introns in the transcript

n_minor_introns

INTEGER, number of minor introns in the transcript

19,440 rows where taxonomy_id = 9999

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CREATE TABLE "transcripts" (
"id" INTEGER,
  "taxonomy_id" INTEGER,
  "transcript_id" TEXT,
  "gene_id" TEXT,
  "chromosome" TEXT,
  "strand" TEXT,
  "start" INTEGER,
  "end" INTEGER,
  "coding_length" INTEGER,
  "introns_per_kbp_cds" REAL,
  "proportion_minor_introns" REAL,
  "n_introns" INTEGER,
  "n_minor_introns" INTEGER
  ,PRIMARY KEY ([id]),
   FOREIGN KEY([taxonomy_id]) REFERENCES [genomes]([taxonomy_id])
);
CREATE INDEX [idx_transcripts_taxonomy_id]
    ON [transcripts] ([taxonomy_id]);
CREATE INDEX [idx_transcripts_gene_id]
    ON [transcripts] ([gene_id]);
CREATE INDEX [idx_transcripts_chromosome]
    ON [transcripts] ([chromosome]);