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)

5 rows where transcript_id = 31282394

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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
174343226 GT-AG 0 0.7531523827288494 54 rna-JXQ802_LOCUS79 31282394 1 437362 437415 Rotaria sordida 392033 ATT|GTTTCTTTTT...AAAAGATTAATA/AAAAGATTAATA...TTTAG|TTG 2 1 2.249
174343227 GT-AG 0 1.000000099473604e-05 57 rna-JXQ802_LOCUS79 31282394 2 437475 437531 Rotaria sordida 392033 AAG|GTAGATCAGG...TTATCATTACTT/TGTTTATTTATC...TATAG|GAC 1 1 10.053
174343228 GT-AG 0 0.0003076359949946 83 rna-JXQ802_LOCUS79 31282394 3 437693 437775 Rotaria sordida 392033 AAA|GTATGATAGT...TTGTTTTTGTTT/TAAATATTGAAT...TTTAG|ATA 0 1 31.349
174343229 GT-AG 0 0.0003453906881602 69 rna-JXQ802_LOCUS79 31282394 4 437894 437962 Rotaria sordida 392033 TTG|GTTTATATTT...ATTTACTTAAAA/TATTTACTTAAA...TCTAG|GTA 1 1 46.958
174343230 GT-AG 0 1.000000099473604e-05 63 rna-JXQ802_LOCUS79 31282394 5 438192 438254 Rotaria sordida 392033 TCA|GTAAGAAATA...TATTTCTTTTTA/TTTCTTTTTATG...TATAG|AAA 2 1 77.249

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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]);