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 = 38490475

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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
213116784 GT-AG 0 1.016389741313622e-05 917 rna-XM_008667295.3 38490475 1 290111827 290112743 Zea mays 4577 AAG|GTAAACAACT...GTACTCTTGTCC/CAAGCACTTACT...TCTAG|ATA 0 1 29.094
213116785 GT-AG 0 0.0322589075843834 617 rna-XM_008667295.3 38490475 2 290111132 290111748 Zea mays 4577 CCG|GTAACTTCCT...GTTCTCTTACTC/TGTTCTCTTACT...CACAG|CTG 0 1 31.255
213116786 GT-AG 0 1.000000099473604e-05 614 rna-XM_008667295.3 38490475 3 290110461 290111074 Zea mays 4577 AAG|GTAAGATCCA...ATGCTCAGGATC/ATCCAATTCAAT...TCCAG|GCT 0 1 32.835
213116787 GT-AG 0 2.341840108470147e-05 76 rna-XM_008667295.3 38490475 4 290108338 290108413 Zea mays 4577 AAG|GTTTGTTCAT...TGTGCATTATCT/CATTATCTGATT...TGCAG|TTC 1 1 89.554
213116788 GT-AG 0 1.000000099473604e-05 81 rna-XM_008667295.3 38490475 5 290108138 290108218 Zea mays 4577 CAG|GTAAATTTGG...TGTATTATACTT/ACGTGTATTATA...TGTAG|GCA 0 1 92.851
213116789 GT-AG 0 0.000633153222591 83 rna-XM_008667295.3 38490475 6 290107983 290108065 Zea mays 4577 CAG|GTAACTTGGA...TGCAATTTAACA/TTTTTCCTCATG...GTTAG|ATT 0 1 94.846
213116790 GT-AG 0 1.000000099473604e-05 328 rna-XM_008667295.3 38490475 7 290107580 290107907 Zea mays 4577 CAG|GTAATTACTG...GATTTTCTAGCA/TAGCAAGTCAAA...TGCAG|GCT 0 1 96.924

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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]);