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 = 32077049

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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
179146897 GT-AG 0 0.0001186812771588 45 rna-XM_008605836.1 32077049 1 1122263 1122307 Saprolegnia diclina 112098 CTC|GTACGTGTTG...ATTGTTTGAGAT/CATTGTTTGAGA...TTTAG|ATT 0 1 38.024
179146898 GT-AG 0 4.533094235402977e-05 47 rna-XM_008605836.1 32077049 2 1122003 1122049 Saprolegnia diclina 112098 ACG|GTACGCGGCG...CAACCCTACACT/CAACCCTACACT...TCTAG|TTG 0 1 45.11
179146899 GT-AG 0 0.0026236046382383 47 rna-XM_008605836.1 32077049 3 1121881 1121927 Saprolegnia diclina 112098 CTC|GTACATCTTG...TGGACCTCAAAC/ATGGACCTCAAA...ATTAG|GTG 0 1 47.605
179146900 GT-AG 0 1.000000099473604e-05 45 rna-XM_008605836.1 32077049 4 1121782 1121826 Saprolegnia diclina 112098 ACG|GTACGTACGC...TACGCCTCCACC/ACCATACACATG...CGTAG|GTG 0 1 49.401
179146901 GT-AG 0 1.000000099473604e-05 49 rna-XM_008605836.1 32077049 5 1121166 1121214 Saprolegnia diclina 112098 CTG|GTACAAGAAT...TGAGATTTGATT/TGAGATTTGATT...TCCAG|GTG 0 1 68.263
179146902 GT-AG 0 0.0018750980762038 51 rna-XM_008605836.1 32077049 6 1120855 1120905 Saprolegnia diclina 112098 TCG|GTATAGTGCT...GTCCCTTGGATT/TCGATCCATACT...GCTAG|CTT 2 1 76.913

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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]);