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 = 20211448

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Suggested facets: dinucleotide_pair, score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
108234521 GC-AG 0 1.000000099473604e-05 32 rna-XM_019609547.1 20211448 1 24313351 24313382 Lupinus angustifolius 3871 AAG|GCAATCTTCT...GATCCACCAATG/GATCCACCAATG...GACAG|AGC 2 1 5.641
108234522 GT-AG 0 1.000000099473604e-05 101 rna-XM_019609547.1 20211448 2 24314660 24314760 Lupinus angustifolius 3871 TGA|GTCAGGATGA...AAACTCTGGACT/TCTGGACTTATG...AATAG|AGA 1 1 42.211
108234523 GC-AG 0 0.0057573638918357 74 rna-XM_019609547.1 20211448 3 24316093 24316166 Lupinus angustifolius 3871 ATG|GCATCTATAC...CATGCCTTTATG/GCTTCTATCATT...CACAG|GCA 1 1 80.355
108234524 GT-AG 0 0.0026931269682409 60 rna-XM_019609547.1 20211448 4 24316284 24316343 Lupinus angustifolius 3871 CAG|GTATACTAAT...TATACTTGGAAG/ATATTACTGATA...GCTAG|ATT 1 1 83.706
108234525 GT-AG 0 1.000000099473604e-05 760 rna-XM_019609547.1 20211448 5 24316519 24317278 Lupinus angustifolius 3871 CAG|GTACATGGAA...TTGTTATTATTT/CTTGTTATTATT...ATAAG|GGT 2 1 88.717
108234526 GT-AG 0 1.000000099473604e-05 2630 rna-XM_019609547.1 20211448 6 24317352 24319981 Lupinus angustifolius 3871 CAA|GTGAGAATAT...ATCAATTTATTT/AATCAATTTATT...TGCAG|GAT 0 1 90.808

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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]);