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 = 2121821

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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
11621351 GT-AG 0 0.0003781482098284 66 rna-XM_009823577.1 2121821 1 2120976 2121041 Aphanomyces astaci 112090 ACG|GTATGGCCTC...GATGTCTTATCG/TGATGTCTTATC...CGTAG|CGG 1 1 6.711
11621352 GT-AG 0 1.000000099473604e-05 70 rna-XM_009823577.1 2121821 2 2120676 2120745 Aphanomyces astaci 112090 AAG|GTATGAAGCA...GTAAAATTGACT/AATTGACTGATC...TACAG|CTG 0 1 13.923
11621353 GT-AG 0 1.000000099473604e-05 46 rna-XM_009823577.1 2121821 3 2120453 2120498 Aphanomyces astaci 112090 ACT|GTACGGAGCT...TCCACCTTCGTA/TCCATGCTCATC...TATAG|GAC 0 1 19.473
11621354 GT-AG 0 1.000000099473604e-05 81 rna-XM_009823577.1 2121821 4 2120291 2120371 Aphanomyces astaci 112090 GAG|GTAAATACCC...AAGTCCTCACAC/AAAGTCCTCACA...TGTAG|AAC 0 1 22.013
11621355 GT-AG 0 1.309305038175685e-05 116 rna-XM_009823577.1 2121821 5 2119395 2119510 Aphanomyces astaci 112090 CAG|GTACGGTTCT...GTGTCCATATTA/ATGGTGATAATT...TGTAG|GTG 0 1 46.472
11621356 GT-AG 0 0.0001554146131734 61 rna-XM_009823577.1 2121821 6 2118165 2118225 Aphanomyces astaci 112090 TCG|GTACGTTGTC...TTGTTTTTTGTG/TGTGGACTTATG...CGTAG|GTA 2 1 83.13

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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]);