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 = 1028926

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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
5357429 GT-AG 0 1.000000099473604e-05 218 rna-AFUS01_LOCUS35 1028926 1 443610 443827 Allacma fusca 39272 CCA|GTAAGTCCGC...TATGCTTCACCA/CTATGCTTCACC...TGTAG|GTT 0 1 4.912
5357430 GT-AG 0 0.0223864472665815 1978 rna-AFUS01_LOCUS35 1028926 2 443934 445911 Allacma fusca 39272 CAA|GTTTCCAATT...TAAAATTTATTG/ATAAAATTTATT...CATAG|GGC 1 1 17.31
5357431 GT-AG 0 7.684039589315226e-05 83 rna-AFUS01_LOCUS35 1028926 3 445974 446056 Allacma fusca 39272 CAG|GTTTGTTGAT...TTGTCCTTACAA/TTTGTCCTTACA...TCCAG|CTC 0 1 24.561
5357432 GT-AG 0 1.000000099473604e-05 96 rna-AFUS01_LOCUS35 1028926 4 446234 446329 Allacma fusca 39272 CCT|GTGAGGCACA...TTGTCAATATTT/GTGATTGTCAAT...CATAG|GGA 0 1 45.263
5357433 GT-AG 0 1.0032060311919845e-05 88 rna-AFUS01_LOCUS35 1028926 5 446405 446492 Allacma fusca 39272 GAG|GTGTGCGTCC...CAGTCCTTGTAC/CTTGTACTAATT...CGTAG|GTA 0 1 54.035
5357434 GT-AG 0 1.2125636477496972e-05 86 rna-AFUS01_LOCUS35 1028926 6 446695 446780 Allacma fusca 39272 TCG|GTTAGCACTA...TATACTTTAACT/TATACTTTAACT...TTCAG|TTT 1 1 77.661
5357435 GT-AG 0 1.000000099473604e-05 96 rna-AFUS01_LOCUS35 1028926 7 446876 446971 Allacma fusca 39272 GAG|GTCAGATATC...ATTTTTTTAAAT/ATTGTACTCACA...TTCAG|AAA 0 1 88.772

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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]);