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 = 5879339

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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
29940356 GT-AG 0 0.045433615394382 50 rna-XM_014946445.1 5879339 1 828344 828393 Calidris pugnax 198806 CCC|GTACGCTCCT...TTGGCTTCAGCG/TTTGGCTTCAGC...CAAAG|ATG 2 1 10.101
29940357 GT-AG 0 1.000000099473604e-05 171 rna-XM_014946445.1 5879339 2 828553 828723 Calidris pugnax 198806 CAG|GTAGGCAAGG...GGCTCCTCAGCC/CGGCTCCTCAGC...CTCAG|CAT 2 1 30.177
29940358 GT-AG 0 1.000000099473604e-05 1673 rna-XM_014946445.1 5879339 3 828786 830458 Calidris pugnax 198806 AAG|GTAAGGCCGG...GTCTTCTTAAAT/TGTCTTCTTAAA...TCTAG|TGT 1 1 38.005
29940359 GT-AG 0 4.904402292626831e-05 4480 rna-XM_014946445.1 5879339 4 830527 835006 Calidris pugnax 198806 AAT|GTAAGCAGAC...TTTGTTTTACTT/CTTTGTTTTACT...CACAG|CAA 0 1 46.591
29940360 GT-AG 0 0.1845448789340301 639 rna-XM_014946445.1 5879339 5 835118 835756 Calidris pugnax 198806 ATT|GTATGCATTT...TGACCTCTGACT/GACACTTTCATT...CCTAG|AAC 0 1 60.606
29940361 GT-AG 0 1.000000099473604e-05 2439 rna-XM_014946445.1 5879339 6 835834 838272 Calidris pugnax 198806 CTC|GTAAGTACCA...GCCTCCGTGGCT/CTGCTTTGCAAA...TCAAG|ATG 2 1 70.328

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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]);