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 = 38490428

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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
213116269 GT-AG 0 1.000000099473604e-05 1533 rna-XM_008662300.4 38490428 1 153296237 153297769 Zea mays 4577 GAG|GTTCGTGGTC...TATTCCTTATGA/TTATTCCTTATG...TTCAG|ATG 2 1 0.71
213116270 GT-AG 0 4.963546380663429e-05 90 rna-XM_008662300.4 38490428 2 153297851 153297940 Zea mays 4577 GAG|GTAACAATTT...TATACTTTTTCT/AGTGGATTGATT...TTTAG|GTT 2 1 2.506
213116271 GT-AG 0 1.000000099473604e-05 115 rna-XM_008662300.4 38490428 3 153297986 153298100 Zea mays 4577 AAA|GTAAGTATGC...TGATTTCTATTT/TTCTATTTCAAT...GGTAG|GGG 2 1 3.504
213116272 GT-AG 0 1.000000099473604e-05 87 rna-XM_008662300.4 38490428 4 153298465 153298551 Zea mays 4577 CCG|GTAATGCTGC...TGTATTTTACCT/ATGTATTTTACC...TGTAG|GGG 0 1 11.577
213116273 GT-AG 0 0.001469459694977 280 rna-XM_008662300.4 38490428 5 153298634 153298913 Zea mays 4577 GAG|GTAACTATGT...TTCTCTTTACAT/GTTCTCTTTACA...TCCAG|GCC 1 1 13.395
213116274 GT-AG 0 0.0003107800937568 98 rna-XM_008662300.4 38490428 6 153298995 153299092 Zea mays 4577 CTG|GTATAATATA...ATTGCCTGACCT/TATTGCCTGACC...GCTAG|GAA 1 1 15.192
213116275 GT-AG 0 0.0001879642951684 496 rna-XM_008662300.4 38490428 7 153300604 153301099 Zea mays 4577 CAG|GTATATAGTT...AGCGTCATATCT/TGATTGCTCACT...TTCAG|CGT 0 1 48.703

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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]);