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 = 14424085

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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
77102277 GT-AG 0 0.2885742090429756 85 rna-XM_006413934.2 14424085 1 8961200 8961284 Eutrema salsugineum 72664 GAG|GTACCCATCG...TTTTCCTCAGAA/AATTGATTCAAT...TGCAG|TTT 0 1 6.311
77102278 GT-AG 0 1.000000099473604e-05 333 rna-XM_006413934.2 14424085 2 8960804 8961136 Eutrema salsugineum 72664 AAG|GTTAGTTTTT...TATACTTTAGTT/TTTGGTTTGATA...TGCAG|ATC 0 1 8.01
77102279 GT-AG 0 0.0990321650281577 138 rna-XM_006413934.2 14424085 3 8960514 8960651 Eutrema salsugineum 72664 TAA|GTATGTTGAT...TGTTTCTTAATG/CTGTTTCTTAAT...TGCAG|ACC 2 1 12.109
77102280 GT-AG 0 7.45069999934279e-05 130 rna-XM_006413934.2 14424085 4 8960258 8960387 Eutrema salsugineum 72664 AAA|GTATTGCCAT...CATTACTTACTA/ACATTACTTACT...TGCAG|GCT 2 1 15.507
77102281 GT-AG 0 1.000000099473604e-05 127 rna-XM_006413934.2 14424085 5 8959929 8960055 Eutrema salsugineum 72664 GAG|GTTGGTCTTA...TGGTCTTTAACT/TGGTCTTTAACT...TGCAG|CCT 0 1 20.955
77102282 GT-AG 0 0.0001158899964662 101 rna-XM_006413934.2 14424085 6 8959713 8959813 Eutrema salsugineum 72664 GAG|GTAAATTTCT...TTGCTTTTGATA/TATATTCTAATT...CACAG|GGT 1 1 24.056
77102283 GT-AG 0 0.0002533807165078 215 rna-XM_006413934.2 14424085 7 8958742 8958956 Eutrema salsugineum 72664 CTC|GTAAGCATCA...TTAATGTTAGCA/ATGAGATTCAAT...TTGAG|GAT 1 1 44.444

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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]);