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 = 15319282

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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
82923446 GT-AG 0 0.0001406926210431 586 rna-gnl|WGS:VWPO|GLAPRA_R08831_mrna 15319282 1 2976687 2977272 Glareola pratincola 43316 GAG|GTCTGTATAA...CTTTTTTTATTT/ACTTTTTTTATT...ATCAG|ATA 0 1 7.042
82923447 GT-AG 0 1.000000099473604e-05 2022 rna-gnl|WGS:VWPO|GLAPRA_R08831_mrna 15319282 2 2974509 2976530 Glareola pratincola 43316 ATG|GTAAATACAG...TATCCCCTGATG/GTTTGTTTAAAA...TAAAG|AAT 0 1 21.69
82923448 GT-AG 0 1.005619587698533e-05 1429 rna-gnl|WGS:VWPO|GLAPRA_R08831_mrna 15319282 3 2972959 2974387 Glareola pratincola 43316 CTA|GTAAGTACCA...GATCTCTCAACT/AGATCTCTCAAC...TTAAG|GTG 1 1 33.052
82923449 GT-AG 0 1.000000099473604e-05 2273 rna-gnl|WGS:VWPO|GLAPRA_R08831_mrna 15319282 4 2970534 2972806 Glareola pratincola 43316 AAG|GTAAGACAAC...TTTTTTTTATTA/TTTTTTTTTATT...TCTAG|AAA 0 1 47.324
82923450 GT-AG 0 1.000000099473604e-05 995 rna-gnl|WGS:VWPO|GLAPRA_R08831_mrna 15319282 5 2969332 2970326 Glareola pratincola 43316 CAG|GTCAGCCAAC...ATTTCCTTGTTT/TGCTTGTTTACA...TGTAG|GAA 0 1 66.761
82923451 GT-AG 0 4.765478728863085e-05 8966 rna-gnl|WGS:VWPO|GLAPRA_R08831_mrna 15319282 6 2960215 2969180 Glareola pratincola 43316 ATA|GTAAGTGTTT...CTTATTTTGACA/CTTATTTTGACA...TCTAG|TTG 1 1 80.939

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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]);