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 = 20211406

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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
108233866 GT-AG 0 1.000000099473604e-05 509 rna-XM_019601928.1 20211406 1 24594358 24594866 Lupinus angustifolius 3871 TTG|GTGAGTCAAA...TATATTTGGATC/ATAGAATTTACA...AACAG|TTA 1 1 15.794
108233867 GT-AG 0 0.00197126756357 83 rna-XM_019601928.1 20211406 2 24594946 24595028 Lupinus angustifolius 3871 CAG|GTACTCAATT...TTAACTTTAATT/TGTATATTAACT...ATCAG|GTT 2 1 17.361
108233868 GT-AG 0 1.000000099473604e-05 240 rna-XM_019601928.1 20211406 3 24595097 24595336 Lupinus angustifolius 3871 ATG|GTAGGAATTT...TTTCCTTTGGAT/CTGTCACTAATT...TATAG|GTT 1 1 18.71
108233869 GT-AG 0 0.0001198645927626 445 rna-XM_019601928.1 20211406 4 24595488 24595932 Lupinus angustifolius 3871 TAG|GTTTGTTTCT...GCTGTTATAATA/GCTGTTATAATA...TACAG|AAT 2 1 21.706
108233870 GT-AG 0 1.000000099473604e-05 4756 rna-XM_019601928.1 20211406 5 24596589 24601344 Lupinus angustifolius 3871 AAG|GTGCGACTAT...TTTTCCATGACC/TTCAGTTTCAAT...TGCAG|AAT 1 1 34.722
108233871 GT-AG 0 1.000000099473604e-05 931 rna-XM_019601928.1 20211406 6 24602023 24602953 Lupinus angustifolius 3871 CAG|GTCTGGTGGT...ATTTCTTTCATT/ATTTCTTTCATT...TTCAG|ATT 1 1 48.175

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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]);