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 = 10007591

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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
55033713 GT-AG 0 0.0002795616034146 101 rna-XM_008443581.2 10007591 1 4167119 4167219 Cucumis melo 3656 TAG|GTATATAATT...AATGCTTTGTTA/ATTAGAATAACC...TGTAG|AAT 1 1 52.523
55033714 GT-AG 0 1.000000099473604e-05 212 rna-XM_008443581.2 10007591 2 4166796 4167007 Cucumis melo 3656 AGG|GTAAGTACTC...TGTTTCTTGTCT/CCTGATCTAATT...ACCAG|GTA 1 1 57.113
55033715 GT-AG 0 0.0026488039230093 88 rna-XM_008443581.2 10007591 3 4166577 4166664 Cucumis melo 3656 AAA|GTACTTTTTC...TTTTTTTTCAAA/TTTTTTTTCAAA...TGTAG|GGA 0 1 62.531
55033716 GT-AG 0 1.000000099473604e-05 146 rna-XM_008443581.2 10007591 4 4166220 4166365 Cucumis melo 3656 TTG|GTTGGTGCCA...TTGTCTTTAATT/TTGTCTTTAATT...TATAG|ATG 1 1 71.257
55033717 GT-AG 0 8.273786475828124e-05 105 rna-XM_008443581.2 10007591 5 4165877 4165981 Cucumis melo 3656 TTA|GTAAGTGTAT...CATTTCTTAGCT/AAATTTTTAATA...TATAG|TGG 2 1 81.1
55033718 GT-AG 0 1.000000099473604e-05 83 rna-XM_008443581.2 10007591 6 4165643 4165725 Cucumis melo 3656 CAT|GTGAGTATTA...ACTAACTTGAAG/TGGAAACTAACT...ACCAG|GCA 0 1 87.345

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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]);