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 = 12947933

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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
69095712 GT-AG 0 0.0007210210365561 133 rna-XM_010913809.3 12947933 1 6071880 6072012 Elaeis guineensis 51953 GTG|GTAATCTCGC...TTTTTGTTAATT/TTTTTGTTAATT...GGCAG|CAA 2 1 1.831
69095713 GT-AG 0 1.034964450231304e-05 2167 rna-XM_010913809.3 12947933 2 6069580 6071746 Elaeis guineensis 51953 CGG|GTTCGTTCTG...TTCTTCTTGCCT/TGTGGATTGACT...TTCAG|GTT 0 1 5.959
69095714 GT-AG 0 0.0004530711878326 2212 rna-XM_010913809.3 12947933 3 6067264 6069475 Elaeis guineensis 51953 GAA|GTATGTAAAA...ATCTTTTTATAA/TATAATCTCATT...ACCAG|GAT 2 1 9.187
69095715 GT-AG 0 0.036020625245914 202 rna-XM_010913809.3 12947933 4 6066890 6067091 Elaeis guineensis 51953 ATG|GTATGTTTTA...ATGTTTTTACTT/CATGTTTTTACT...ATTAG|GTG 0 1 14.525
69095716 GT-AG 0 1.000000099473604e-05 98 rna-XM_010913809.3 12947933 5 6066651 6066748 Elaeis guineensis 51953 CTG|GTAAGATATA...GGTTTCTTGAAT/ATAAAACTGACA...AGCAG|AAT 0 1 18.901
69095717 GT-AG 0 1.000000099473604e-05 103 rna-XM_010913809.3 12947933 6 6066343 6066445 Elaeis guineensis 51953 CAG|GTATGAGAAG...CCTTTTATGATT/CCTTTTATGATT...AACAG|AAA 1 1 25.264

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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]);