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 = 4181809

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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
21587440 GT-AG 0 0.0211029399140677 867 rna-XM_010682115.2 4181809 1 17945959 17946825 Beta vulgaris 161934 CAG|GTATTTTTTT...TCTATTTTACTT/TTCTATTTTACT...TGCAG|GCA 0 1 1.412
21587441 GT-AG 0 0.0001585605582187 1991 rna-XM_010682115.2 4181809 2 17943881 17945871 Beta vulgaris 161934 AGT|GTAAGTTGGA...TGTCTCTTATTC/ATGTTTTTTATT...CACAG|GAT 0 1 3.972
21587442 GT-AG 0 1.000000099473604e-05 118 rna-XM_010682115.2 4181809 3 17943673 17943790 Beta vulgaris 161934 ACT|GTGAGTACCC...GTTCTATTATTT/TATTATTTCAAT...CCCAG|GCT 0 1 6.62
21587443 GT-AG 0 1.000000099473604e-05 80 rna-XM_010682115.2 4181809 4 17943506 17943585 Beta vulgaris 161934 CTG|GTTGGTGACA...GGTATATTATCC/TAGAATTTGAAT...TTTAG|ATC 0 1 9.179
21587444 GT-AG 0 0.0008126214893846 91 rna-XM_010682115.2 4181809 5 17943295 17943385 Beta vulgaris 161934 CAT|GTAACGCTTT...TAGTGCTTAAAA/ATTTTGTCCATT...TGCAG|GAC 0 1 12.71
21587445 GT-AG 0 0.0124553114634923 81 rna-XM_010682115.2 4181809 6 17941114 17941194 Beta vulgaris 161934 CAG|GTATTCATAT...TCTTGTTTAATT/TCTTGTTTAATT...GTAAG|GTT 0 1 74.492
21587446 GT-AG 0 0.000423496430061 451 rna-XM_010682115.2 4181809 7 17940516 17940966 Beta vulgaris 161934 CAG|GTTCTTTTCC...TATTCTTTAATT/TATTCTTTAATT...TTCAG|CTT 0 1 78.817
21587447 GT-AG 0 1.000000099473604e-05 392 rna-XM_010682115.2 4181809 8 17939567 17939958 Beta vulgaris 161934 CAG|GTAAAAGTTG...TAAGGTTTGACA/TAAGGTTTGACA...TGCAG|CCG 2 1 95.204

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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]);