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 = 28321233

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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
157404497 GT-AG 0 1.000000099473604e-05 54113 rna-gnl|WGS:JMFS|mrna.N338_11356 28321233 1 25479 79591 Podiceps cristatus 345573 ATG|GTAAGAAAAT...AATTTATTATCT/TATTATCTAAAT...CTTAG|GAA 0 1 8.54
157404498 GT-AG 0 1.000000099473604e-05 33750 rna-gnl|WGS:JMFS|mrna.N338_11356 28321233 2 79736 113485 Podiceps cristatus 345573 AAG|GTAGGATCAC...GACTCATTAATT/AAAAGACTCATT...TTCAG|GTT 0 1 15.152
157404499 GT-AG 0 0.0001030151086376 1133 rna-gnl|WGS:JMFS|mrna.N338_11356 28321233 3 113692 114824 Podiceps cristatus 345573 GAG|GTAGGTTTCA...TTTTTCTTGGTG/ACCAGTTTAAAT...ACTAG|ACC 2 1 24.61
157404500 GT-AG 0 1.000000099473604e-05 1464 rna-gnl|WGS:JMFS|mrna.N338_11356 28321233 4 115099 116562 Podiceps cristatus 345573 CAG|GTAGGGAAAA...CTAACTTTGATT/CTGATGCTAACT...TTCAG|ATA 0 1 37.19
157404501 GT-AG 0 2.7242638550344675e-05 3242 rna-gnl|WGS:JMFS|mrna.N338_11356 28321233 5 116755 119996 Podiceps cristatus 345573 CAG|GTACTATTGC...TATGTTTTATAT/TTTATTCTAAGC...TATAG|GAA 0 1 46.006

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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]);