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 = 2121846

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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
11621555 GT-AG 0 1.000000099473604e-05 98 rna-XM_009822661.1 2121846 1 350696 350793 Aphanomyces astaci 112090 CAG|GTGTGTGTGG...ACAATTGTGAAT/AGCAACTTCACA...TGTAG|GAA 0 1 10.576
11621556 GT-AG 0 1.000000099473604e-05 73 rna-XM_009822661.1 2121846 2 351365 351437 Aphanomyces astaci 112090 CAG|GTGCGTCGTA...AAACCATTGAAG/AATTGTATGAAC...GCTAG|CCA 1 1 30.506
11621557 GT-AG 0 1.000000099473604e-05 47 rna-XM_009822661.1 2121846 3 351611 351657 Aphanomyces astaci 112090 CAT|GTACTACGAT...TTCCTCGTTGCG/AGAATGTTCACA...GGTAG|GAA 0 1 36.545
11621558 GT-AG 0 1.000000099473604e-05 48 rna-XM_009822661.1 2121846 4 352225 352272 Aphanomyces astaci 112090 CAA|GTACGACACG...TCTACCTTCACA/TCTACCTTCACA...TTCAG|GAG 0 1 56.335
11621559 GT-AG 0 1.000000099473604e-05 43 rna-XM_009822661.1 2121846 5 352495 352537 Aphanomyces astaci 112090 GAG|GTACGACGAC...CATCACATGATT/ATATGCATCACA...CCTAG|CTC 0 1 64.084
11621560 GT-AG 0 5.389434034855439e-05 280 rna-XM_009822661.1 2121846 6 352996 353275 Aphanomyces astaci 112090 CAG|GTATGTATCG...AAACTCTTGTAG/ATGTGATTGATT...TGTAG|GTG 2 1 80.07

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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]);