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 = 32765300

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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
183237387 GT-AG 0 1.002205277590732 112 rna-XM_004951216.3 32765300 2 969632 969743 Setaria italica 4555 CAG|GTATCTTGTT...TATTCTTTTGCT/CTATTTCTAAGA...TGCAG|GGC 0 1 52.949
183237388 GT-AG 0 2.817224529081445e-05 115 rna-XM_004951216.3 32765300 3 969319 969433 Setaria italica 4555 AAA|GTAAGTATTG...GTTACTTTGAAA/GAAATACTAATT...CTCAG|GAG 0 1 57.323
183237389 GT-AG 0 4.0528116290231455e-05 292 rna-XM_004951216.3 32765300 4 968850 969141 Setaria italica 4555 CAA|GTAAGTTAAC...TCGACTTTAATT/TATGATTTAACT...AACAG|GGA 0 1 61.233
183237390 GT-AG 0 0.0004150076310419 83 rna-XM_004951216.3 32765300 5 968623 968705 Setaria italica 4555 GAA|GTAAGTTGTC...ATTGTTTTAACC/ATTGTTTTAACC...AACAG|AAG 0 1 64.414
183237391 GT-AG 0 1.000000099473604e-05 86 rna-XM_004951216.3 32765300 6 968324 968409 Setaria italica 4555 AAG|GTGAGTTCTG...AACATATTAACA/TCTATTCTGATT...AACAG|GAT 0 1 69.119
183249914 GT-AG 0 1.000000099473604e-05 1301 rna-XM_004951216.3 32765300 1 971856 973156 Setaria italica 4555 ACT|GTGAGTGCCC...TTGTTCTTATTC/CTTGTTCTTATT...TGCAG|GTA   0 7.886

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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]);