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)

7 rows where transcript_id = 9129022

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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
49483214 GT-AG 0 0.000250811277892 1089 rna-XM_004673904.2 9129022 3 74932103 74933191 Condylura cristata 143302 CAG|GTAACTGATG...TGTGTCTTAGAG/CATGAACTGAAT...TACAG|ATG 0 1 71.086
49483215 GT-AG 0 1.000000099473604e-05 3567 rna-XM_004673904.2 9129022 4 74928381 74931947 Condylura cristata 143302 AGG|GTAAGCAAAC...GGATCCTTTTTG/AAGTATTTGAAA...AACAG|GTA 2 1 73.164
49483216 GT-AG 0 1.000000099473604e-05 3507 rna-XM_004673904.2 9129022 5 74924698 74928204 Condylura cristata 143302 AAG|GTACGGGTCT...ATTTTGGTAACC/ATTTTGGTAACC...TCCAG|GAA 1 1 75.523
49483217 GT-AG 0 0.0021362522057616 795 rna-XM_004673904.2 9129022 6 74923801 74924595 Condylura cristata 143302 CAG|GTATTTCATA...TGGATCTTGATC/TCTAAACTTACT...TTCAG|AAA 1 1 76.89
49483218 GT-AG 0 7.913594550468065e-05 2144 rna-XM_004673904.2 9129022 7 74920761 74922904 Condylura cristata 143302 CCC|GTAAGTATAA...GGGTCCTAAATG/TGGGTCCTAAAT...TGCAG|AAC 0 1 88.901
49488637 GT-AG 0 1.000000099473604e-05 5337 rna-XM_004673904.2 9129022 1 74939454 74944790 Condylura cristata 143302 CAG|GTTAATAACT...TATTTCCTAACG/TATTTCCTAACG...CCCAG|GAA   0 1.314
49488638 GT-AG 0 1.5636407993106422e-05 667 rna-XM_004673904.2 9129022 2 74938742 74939408 Condylura cristata 143302 CAG|GTAATTATTA...GTTTCCTTTTCT/GACAATCTCATT...TTCAG|ATG   0 1.917

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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]);