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)

8 rows where transcript_id = 37957322

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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
209597136 GT-AG 0 0.5964922915377562 448 rna-XM_022784236.1 37957322 1 9541697 9542144 Vigna radiata 157791 TGG|GTATGCTACT...ACTTCTTTGATT/ACTTCTTTGATT...GACAG|AAA 2 1 7.75
209597137 GT-AG 0 1.000000099473604e-05 115 rna-XM_022784236.1 37957322 2 9540483 9540597 Vigna radiata 157791 ACA|GTAAGACTGA...GTATGCTTACAT/TGTATGCTTACA...AACAG|GGG 0 1 25.422
209597138 GT-AG 0 1.000000099473604e-05 336 rna-XM_022784236.1 37957322 3 9538971 9539306 Vigna radiata 157791 CAG|GTTGTTTTTA...CTGTACTTAATA/ACTGTACTTAAT...CTCAG|GAA 0 1 44.332
209597139 GT-AG 0 0.0004974284828936 2684 rna-XM_022784236.1 37957322 4 9535611 9538294 Vigna radiata 157791 AGG|GTATTGAATT...AGTATCTTGACT/TCTTGACTTACT...AACAG|AAT 1 1 55.202
209597140 GT-AG 0 1.0611151428839591e-05 298 rna-XM_022784236.1 37957322 5 9535094 9535391 Vigna radiata 157791 AAG|GTAATTTGTG...ACACTTTTAAAA/TGGTTTCTGATT...TTCAG|GTT 1 1 58.723
209597141 GT-AG 0 1.000000099473604e-05 857 rna-XM_022784236.1 37957322 6 9534079 9534935 Vigna radiata 157791 AAG|GTTAGTGTAT...ATTTTCTGATTC/GATTTTCTGATT...GCCAG|TTT 0 1 61.264
209597142 GT-AG 0 0.0059298864770184 728 rna-XM_022784236.1 37957322 7 9533210 9533937 Vigna radiata 157791 CAT|GTATGCCACT...ACTCTTGTGACG/TGTTTATTGAGT...GGCAG|TTG 0 1 63.531
209597143 GT-AG 0 1.000000099473604e-05 181 rna-XM_022784236.1 37957322 8 9532900 9533080 Vigna radiata 157791 GGA|GTAAGAAGTT...CATCCTTTGAAT/ATTTCTTTTACT...TCCAG|TGG 0 1 65.605

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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]);