introns

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

id
INTEGER (primary key), globally unique identifier for each intron
dinucleotide_pair
TEXT, terminal dinucleotide sequences of the intron
is_minor
INTEGER, indicates if the intron is a minor intron (1) or not (0)
score
REAL, score representing the probability (0-100%) of the intron being minor
length
INTEGER, length of the intron in base pairs
transcript_id
INTEGER (foreign key referencing transcripts(id)), parent transcript
ordinal_index
INTEGER, ordinal position of the intron within the transcript (e.g., 3 for the third intron)
start
INTEGER, start position of the intron in the genome
end
INTEGER, end position of the intron in the genome
taxonomy_id
INTEGER (foreign key referencing genomes(taxonomy_id)), NCBI taxonomy identifier for species
scored_motifs
TEXT, motifs scored for the intron
phase
INTEGER, phase of the intron in coding sequence (0, 1, or 2 or null for introns outside of coding sequence)
in_cds
INTEGER, indicates if the intron is within the coding sequence (1) or not (0; e.g., UTR introns)
relative_position
REAL, relative position of the intron within the transcript (as a percentage of coding length)

4 rows where transcript_id = 1013776

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id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
5251578 GT-AG 0 1.000000099473604e-05 406 rna-gnl|WGS:VXAV|ALELAT_R11780_mrna 1013776 1 77957 78362 Alectura lathami 81907 AAG|GTGAGCTCCT...GTGCGCTGAGTG/TGTGCGCTGAGT...TGCAG|GAT 0 1 19.935
5251579 GT-AG 0 2.809409600421009e-05 601 rna-gnl|WGS:VXAV|ALELAT_R11780_mrna 1013776 2 78476 79076 Alectura lathami 81907 AAG|GTAGCAAGCA...TTGTTTTTGTTT/GTTAGTGTAACA...CTTAG|GTT 2 1 32.244
5251580 GT-AG 0 4.1637100739761335e-05 254 rna-gnl|WGS:VXAV|ALELAT_R11780_mrna 1013776 3 79270 79523 Alectura lathami 81907 TGG|GTACGGTGCC...GTTTTCTTACAC/TGTTTTCTTACA...AATAG|AAA 0 1 53.268
5251581 GT-AG 0 1.3099772772829508e-05 462 rna-gnl|WGS:VXAV|ALELAT_R11780_mrna 1013776 4 79767 80228 Alectura lathami 81907 AAG|GTAAACCTCC...GGTTCATTCACT/GGTTCATTCACT...CCCAG|GTC 0 1 79.739

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CREATE TABLE "introns" (
"id" INTEGER,
  "dinucleotide_pair" TEXT,
  "is_minor" INTEGER,
  "score" REAL,
  "length" INTEGER,
  "transcript_id" INTEGER,
  "ordinal_index" INTEGER,
  "start" INTEGER,
  "end" INTEGER,
  "taxonomy_id" INTEGER,
  "scored_motifs" TEXT,
  "phase" INTEGER,
  "in_cds" INTEGER,
  "relative_position" REAL
  ,PRIMARY KEY ([id]),
   FOREIGN KEY([transcript_id]) REFERENCES [transcripts]([id]),
   FOREIGN KEY([taxonomy_id]) REFERENCES [genomes]([taxonomy_id])
);
CREATE INDEX [idx_introns_transcript_id]
    ON [introns] ([transcript_id]);
CREATE INDEX [idx_introns_taxonomy_id]
    ON [introns] ([taxonomy_id]);
CREATE INDEX [idx_introns_phase]
    ON [introns] ([phase]);
CREATE INDEX [idx_introns_is_minor]
    ON [introns] ([is_minor]);
CREATE INDEX [idx_introns_dinucleotide_pair]
    ON [introns] ([dinucleotide_pair]);
CREATE INDEX [idx_introns_score]
    ON [introns] ([score]);
CREATE INDEX [idx_introns_in_cds]
    ON [introns] ([in_cds]);