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)

7 rows where transcript_id = 4793049

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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
24940245 GT-AG 0 1.000000099473604e-05 2363 Brast01G206100.1.v0.1.stacei 4793049 1 13396201 13398563 Brachypodium stacei 1071399 GAG|GTATGGAATT...TATGACTTATTG/TTATGACTTATT...TACAG|ATC 2 1 9.175
24940246 GT-AG 0 1.000000099473604e-05 116 Brast01G206100.1.v0.1.stacei 4793049 2 13401703 13401818 Brachypodium stacei 1071399 CAG|GTAATTGATG...AATTTCTCATCC/TAATTTCTCATC...AACAG|GAC 0 1 87.435
24940247 GT-AG 0 0.0004314918152155 178 Brast01G206100.1.v0.1.stacei 4793049 3 13401883 13402060 Brachypodium stacei 1071399 AAG|GTATTGCTAA...TTTGCCTTATTT/TTGTTATTTATT...TACAG|TAG 1 1 89.03
24940248 GT-AG 0 12.026172467088482 89 Brast01G206100.1.v0.1.stacei 4793049 4 13402132 13402220 Brachypodium stacei 1071399 GCG|GTATCCTCAA...TATTTCTTCGTG/GTGGTGTTAATG...TCCAG|GAA 0 1 90.8
24940249 GT-AG 0 1.000000099473604e-05 100 Brast01G206100.1.v0.1.stacei 4793049 5 13402287 13402386 Brachypodium stacei 1071399 CAT|GTAAGACAAT...TCTTTCTTAATA/AATATTCTTATC...TACAG|AGA 0 1 92.446
24940250 GT-AG 0 0.0201638192480919 2354 Brast01G206100.1.v0.1.stacei 4793049 6 13402477 13404830 Brachypodium stacei 1071399 TAT|GTACGCATTT...GTTTTCTTCTTC/AATTAAATTATA...GGCAG|ATA 0 1 94.69
24940251 GT-AG 0 1.000000099473604e-05 216 Brast01G206100.1.v0.1.stacei 4793049 7 13405008 13405223 Brachypodium stacei 1071399 AAG|GTGCGTATGT...ATTGCAATAACC/CCGGGGCTAATT...TGCAG|GAA 0 1 99.102

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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]);