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 = 10029632

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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
55135361 GT-AG 0 0.0018186330567563 121 rna-XM_031889650.1 10029632 1 15512936 15513056 Cucumis sativus 3659 AGG|GTACCAATTC...TTTCTATTATCA/ATTAATCTCATA...TGTAG|GCT 1 1 75.023
55135362 GT-AG 0 1.000000099473604e-05 96 rna-XM_031889650.1 10029632 2 15513215 15513310 Cucumis sativus 3659 GAT|GTGGGTTTGT...TGTCTTTTACCA/TAGTTATTCACT...CCCAG|GAT 0 1 78.67
55135363 GT-AG 0 1.000000099473604e-05 102 rna-XM_031889650.1 10029632 3 15513383 15513484 Cucumis sativus 3659 CAG|GTAATAATTA...TTTTTCTTCTTT/TCCATCCTAACA...CTTAG|GTA 0 1 80.332
55135364 GT-AG 0 9.086395779718584e-05 103 rna-XM_031889650.1 10029632 4 15513638 15513740 Cucumis sativus 3659 ATG|GTTGTTCTTT...TGTTCCTTGACT/GTCCTTTTTATT...ACCAG|AGA 0 1 83.864
55135365 GT-AG 0 0.0018164015218863 104 rna-XM_031889650.1 10029632 5 15513905 15514008 Cucumis sativus 3659 AAA|GTAACAATTG...TCACCCTTAGAT/TATATCTTCACC...TACAG|GAG 2 1 87.65
55135366 GT-AG 0 1.313338107557164e-05 2038 rna-XM_031889650.1 10029632 6 15514157 15516194 Cucumis sativus 3659 AAG|GTTTGTTGTT...AGAGCTTTGTTT/GCTTTGTTTATG...TTTAG|GTT 0 1 91.066
55135367 GT-AG 0 0.0024298159690995 88 rna-XM_031889650.1 10029632 7 15516318 15516405 Cucumis sativus 3659 AAG|GTATACTAAT...GATATGTTACTT/TGATATGTTACT...TGTAG|GTC 0 1 93.906
55135368 GT-AG 0 0.0002540978965766 156 rna-XM_031889650.1 10029632 8 15516494 15516649 Cucumis sativus 3659 TAG|GTAAACCTTT...ATTTTCTCAACT/AATTTTCTCAAC...TTCAG|GTG 1 1 95.937

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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]);