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)

6 rows where transcript_id = 2140978

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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
11677118 GT-AG 0 5.81620453795164e-05 43 rna-gnl|WGS:JAHQRK|AC1031_000850-T1_mrna 2140978 1 2525543 2525585 Aphanomyces cochlioides 112091 AAG|GTATGGATAT...CCGATCTTGAAG/CCGATCTTGAAG...CGTAG|ATT 0 1 13.442
11677119 GT-AG 0 1.000000099473604e-05 44 rna-gnl|WGS:JAHQRK|AC1031_000850-T1_mrna 2140978 2 2525787 2525830 Aphanomyces cochlioides 112091 GTG|GTAAGAAAAC...AGGTCTTTATAT/TAGGTCTTTATA...CATAG|GAA 0 1 18.39
11677120 GT-AG 0 1.000000099473604e-05 41 rna-gnl|WGS:JAHQRK|AC1031_000850-T1_mrna 2140978 3 2526017 2526057 Aphanomyces cochlioides 112091 CAG|GTAAGCAACA...TGTTCTTTCGTG/TCTTTCGTGAAA...TGCAG|AGT 0 1 22.969
11677121 GT-AG 0 1.4799258177530697e-05 38 rna-gnl|WGS:JAHQRK|AC1031_000850-T1_mrna 2140978 4 2526216 2526253 Aphanomyces cochlioides 112091 TTG|GTACGTACGA...TGTACTTCAATT/CAATTTCTAATG...TGTAG|GTA 2 1 26.859
11677122 GT-AG 0 0.0002735134566989 42 rna-gnl|WGS:JAHQRK|AC1031_000850-T1_mrna 2140978 5 2527056 2527097 Aphanomyces cochlioides 112091 TCT|GTACGTAAAT...CGAATCTTACCA/TCGAATCTTACC...CTTAG|GAA 0 1 46.603
11677123 GT-AG 0 1.000000099473604e-05 45 rna-gnl|WGS:JAHQRK|AC1031_000850-T1_mrna 2140978 6 2527229 2527273 Aphanomyces cochlioides 112091 TTG|GTAAGACTAT...TCATACGTGACG/CGAGGCTTCATA...TACAG|GTC 2 1 49.828

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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]);