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 = 29320799

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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
163356513 GT-AG 0 1.000000099473604e-05 367 rna-XM_021949293.1 29320799 1 35746 36112 Prunus avium 42229 CAG|GTGATTTCTG...CATTTTTTATTT/GCATTTTTTATT...TTCAG|TGC 1 1 8.473
163356514 GT-AG 0 2.653893591985815e-05 90 rna-XM_021949293.1 29320799 2 36202 36291 Prunus avium 42229 ATG|GTAGGTTCTC...GTGATTTTAGTG/ATTTCATTCATT...TGCAG|GTT 0 1 14.706
163356515 GT-AG 0 0.00238021040722 129 rna-XM_021949293.1 29320799 3 36592 36720 Prunus avium 42229 CAG|GTACATTTTA...CAAGTCTTGAAC/AAATTTCTCAAG...TGCAG|GCA 0 1 35.714
163356516 GT-AG 0 1.000000099473604e-05 157 rna-XM_021949293.1 29320799 4 36823 36979 Prunus avium 42229 GGG|GTAAGATATA...TTGTTTTTGATA/TTGTTTTTGATA...GTCAG|TTG 0 1 42.857
163356517 GT-AG 0 4.904132957807995e-05 107 rna-XM_021949293.1 29320799 5 37175 37281 Prunus avium 42229 ATG|GTTTGTATCT...TCCTCATTAATT/GTTTTCCTCATT...TGCAG|GTT 0 1 56.513
163356518 GT-AG 0 0.8327075643824153 932 rna-XM_021949293.1 29320799 6 37573 38504 Prunus avium 42229 TGT|GTATGTTTAT...TAACCTTTAGTT/GTTCGTCTCACC...GTCAG|TGT 0 1 76.891
163356519 GT-AG 0 1.000000099473604e-05 351 rna-XM_021949293.1 29320799 7 38692 39042 Prunus avium 42229 CTG|GTTGGACTCT...GTTCTTTTGACT/GTTCTTTTGACT...TGTAG|GTG 1 1 89.986
163356520 GT-AG 0 1.000000099473604e-05 82 rna-XM_021949293.1 29320799 8 39090 39171 Prunus avium 42229 AAG|GTGAGATAGG...TGCGCTTTAACA/CATTTTCTAAGA...TTCAG|GGT 0 1 93.277

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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]);