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 = 5879329

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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
29940299 GT-AG 0 1.000000099473604e-05 781 rna-XM_014950274.1 5879329 1 332718 333498 Calidris pugnax 198806 CGG|GTGAGCGTCT...CTTCCCTTTTTT/GTGCTGCTCACA...TACAG|GGA 2 1 7.843
29940300 GT-AG 0 1.000000099473604e-05 1814 rna-XM_014950274.1 5879329 2 333581 335394 Calidris pugnax 198806 GGG|GTAAGTGTGG...GTGGCCTCATCT/GGTGGCCTCATC...TGCAG|TTC 0 1 14.834
29940301 GT-AG 0 1.3156862998156416e-05 2874 rna-XM_014950274.1 5879329 3 335518 338391 Calidris pugnax 198806 GCT|GTCAGCATAT...GGAGCTGTGACG/ACGGGGCTAAGG...GACAG|TCC 0 1 25.32
29940302 GT-AG 0 6.527453575145745e-05 192 rna-XM_014950274.1 5879329 4 338581 338772 Calidris pugnax 198806 AAG|GTAACGGGCC...GGTACCTTAATG/TAATGACTTATT...TACAG|ATC 0 1 41.432
29940303 GT-AG 0 1.000000099473604e-05 76 rna-XM_014950274.1 5879329 5 338945 339020 Calidris pugnax 198806 TAG|GTAGGAGGTG...TTCTCCTTCCCC/GGGTGACTAACA...TTTAG|GGG 1 1 56.095
29940304 GT-AG 0 1.000000099473604e-05 1194 rna-XM_014950274.1 5879329 6 339170 340363 Calidris pugnax 198806 GAG|GTGAGGGCGA...CTCTCTGTAACT/CTCTCTGTAACT...CCCAG|GTT 0 1 68.798

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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]);