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)

7 rows where transcript_id = 33469706

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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
187538449 GT-AG 0 0.0445498066903788 118 rna-XM_021455789.1 33469706 2 73427528 73427645 Sorghum bicolor 4558 GAG|GTATGCTCCT...ACATTCTTATTC/TTCTTATTCATG...TGTAG|AAA 0 1 49.683
187538450 GT-AG 0 0.0002522374159905 418 rna-XM_021455789.1 33469706 3 73426991 73427408 Sorghum bicolor 4558 CAG|GTACTCCCTA...ATTTTTTTCATA/ATTTTTTTCATA...TGTAG|TCA 2 1 52.114
187538451 GT-AG 0 8.662509978090422e-05 178 rna-XM_021455789.1 33469706 4 73425094 73425271 Sorghum bicolor 4558 CAG|GTAAACATTA...AAACCTTTACTT/CTTTACTTTATT...CACAG|CAC 2 1 87.232
187538452 GT-AG 0 1.000000099473604e-05 89 rna-XM_021455789.1 33469706 5 73424956 73425044 Sorghum bicolor 4558 AAG|GTTAGTACAA...ATTATCTTGACA/ATTATCTTGACA...AACAG|GAT 0 1 88.233
187538453 GT-AG 0 5.426730875288912e-05 133 rna-XM_021455789.1 33469706 6 73424581 73424713 Sorghum bicolor 4558 TAA|GTAAGTCTCC...ACCACCTTATTG/ATTTTTCTGATT...ACTAG|CCC 2 1 93.177
187538454 GT-AG 0 3.949953122707824e-05 1079 rna-XM_021455789.1 33469706 7 73423397 73424475 Sorghum bicolor 4558 AAG|GTATGTGATG...TCCTTTTTGGCT/TTTTGGCTGAAA...TACAG|TTT 2 1 95.322
187558129 GT-AG 0 1.000000099473604e-05 1640 rna-XM_021455789.1 33469706 1 73430090 73431729 Sorghum bicolor 4558 GAG|GTAGGTCACG...ATGTACTTATAT/TTCTTCCTCATT...TGCAG|TCT   0 4.637

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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]);