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)

5 rows where transcript_id = 29402375

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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
163707598 GT-AG 0 1.000000099473604e-05 514 rna-XM_007227172.2 29402375 1 35935911 35936424 Prunus persica 3760 TGG|GTAATTACTA...CTGTGTTTAATT/CTGTGTTTAATT...GGCAG|GCA 2 1 13.542
163707599 GT-AG 0 0.0002263027021094 255 rna-XM_007227172.2 29402375 2 35937545 35937799 Prunus persica 3760 TCT|GTAAGTCCTT...CTTTTCTTACTT/CCTTTTCTTACT...AACAG|GGA 0 1 38.991
163707600 GT-AG 0 0.0002764671625029 136 rna-XM_007227172.2 29402375 3 35938079 35938214 Prunus persica 3760 AAG|GTATAATAAT...TGGATTTTAATT/TGGATTTTAATT...AACAG|TTT 0 1 45.331
163707601 GT-AG 0 1.000000099473604e-05 110 rna-XM_007227172.2 29402375 4 35939016 35939125 Prunus persica 3760 CAG|GTTAATCCTT...ACAAATTTGACC/ACAAATTTGACC...TATAG|GGA 0 1 63.531
163707602 GT-AG 0 1.000000099473604e-05 127 rna-XM_007227172.2 29402375 5 35940077 35940203 Prunus persica 3760 CAG|GTCAGTCTCT...CTGGCTCTACAT/AATGTAATGATT...AATAG|GGA 0 1 85.14

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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]);