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 = 38490393

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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
213115632 GT-AG 0 0.0001237269348246 90 rna-NM_001348667.1 38490393 1 69112639 69112728 Zea mays 4577 AAG|GTGCCAATCT...TTTGCCTTATTT/TTTTGCCTTATT...ATCAG|GCT 0 1 66.549
213115633 GT-AG 0 0.0017988669899022 77 rna-NM_001348667.1 38490393 2 69112974 69113050 Zea mays 4577 TCA|GTATGTAGAT...AGTTCTTGAATC/GGGTCACTCACA...TACAG|GCC 2 1 70.148
213115634 GT-AG 0 1.000000099473604e-05 3731 rna-NM_001348667.1 38490393 3 69113199 69116929 Zea mays 4577 CAG|GTAGATTGCT...ATTTATTTATTT/TATTTATTTATT...TGTAG|GTC 0 1 72.323
213115635 GT-AG 0 0.0001647742683831 75 rna-NM_001348667.1 38490393 4 69117117 69117191 Zea mays 4577 TTG|GTAAGCTGCA...TGTGACTTGACT/TTTATTGTGACT...ACCAG|GGG 1 1 75.07
213115636 GT-AG 0 4.37421893641397e-05 92 rna-NM_001348667.1 38490393 5 69117507 69117598 Zea mays 4577 GAG|GTATGATCTT...CTATATTTATTG/GCTATATTTATT...AGCAG|GGG 1 1 79.697
213115637 GT-AG 0 0.0145885652299308 128 rna-NM_001348667.1 38490393 6 69118288 69118415 Zea mays 4577 CAG|GTATGCATTT...GCTTTCTTCATT/GCTTTCTTCATT...TCCAG|ACA 0 1 89.819

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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]);