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 = 1415859

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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
7709012 GT-AG 0 1.000000099473604e-05 40 rna-XM_020000102.1 1415859 1 481276 481315 Amphimedon queenslandica 400682 AAT|GTAAGAATTA...AAAAAATTAATG/AAAAAATTAATG...TGCAG|ATG 1 1 10.675
7709013 GT-AG 0 3.079813919841944e-05 668 rna-XM_020000102.1 1415859 2 481384 482051 Amphimedon queenslandica 400682 TAT|GTAAGTTCAT...TTTTTTGTAATA/TTTTTTGTAATA...TGTAG|AGT 0 1 25.49
7709014 GT-AG 0 1.000000099473604e-05 4074 rna-XM_020000102.1 1415859 3 482113 486186 Amphimedon queenslandica 400682 AAG|GTAATGCCTG...CATTTTTTACTT/ATTTTTCTAATC...TTTAG|TTC 1 1 38.78
7709015 GT-AG 0 6.376086893818276e-05 53 rna-XM_020000102.1 1415859 4 486219 486271 Amphimedon queenslandica 400682 GAG|GTAGACATTG...TTGCATTTATTT/CATTTATTTACA...TGTAG|GTC 0 1 45.752
7709016 GT-AG 0 0.0047223869705941 10101 rna-XM_020000102.1 1415859 5 486386 496486 Amphimedon queenslandica 400682 CAA|GTAAGCTGTT...GTGTCTTTAATA/GTCCATTTCATT...TTTAG|ATA 0 1 70.588
7709017 GT-AG 0 1.4410063165318336e-05 17055 rna-XM_020000102.1 1415859 6 496552 513606 Amphimedon queenslandica 400682 TAG|GTAAGCAATT...AATTTCTTATTG/CAATTTCTTATT...TTTAG|GAC 2 1 84.749

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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]);