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 = 1565140

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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
8696609 GT-AG 0 0.0763981994371938 5244 rna-XM_020236187.1 1565140 1 13268090 13273333 Ananas comosus 4615 CTG|GTACCCCCCC...GTTGTTTTAAGG/GTTGTTTTAAGG...CGCAG|GGC 0 1 8.453
8696610 GT-AG 0 0.0017660959737133 180 rna-XM_020236187.1 1565140 2 13267392 13267571 Ananas comosus 4615 CAA|GTATGTTCAC...ATTTCATTTTCT/ACCAATTTCATT...TGTAG|ATC 2 1 25.04
8696611 GT-AG 0 1.7816797059063225e-05 2164 rna-XM_020236187.1 1565140 3 13264453 13266616 Ananas comosus 4615 GCA|GTTTTGTGAT...GGATTCGGAGCC/GAGCCGCTCATC...CAGAG|CCG 0 1 49.856
8696612 GT-AG 0 7.317466881221069e-05 1439 rna-XM_020236187.1 1565140 4 13262929 13264367 Ananas comosus 4615 TCG|GTAATCCCCT...CCTTTCGTGATA/TGATATCTAACG...TGCAG|GTG 1 1 52.578
8696613 GT-AG 0 1.000000099473604e-05 963 rna-XM_020236187.1 1565140 5 13261748 13262710 Ananas comosus 4615 CTG|GTGCGTTTTC...TCTGTTTTATGG/ATCTGTTTTATG...ACCAG|GGC 0 1 59.558
8696614 GT-AG 0 1.000000099473604e-05 336 rna-XM_020236187.1 1565140 6 13260936 13261271 Ananas comosus 4615 GAA|GTAAGATCGT...TTTTTTTTAATT/TTTTTTTTAATT...TGTAG|GAC 2 1 74.8

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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]);