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 = 14698706

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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
78945630 GT-AG 0 1.000000099473604e-05 518 rna-XM_004287830.2 14698706 1 9234892 9235409 Fragaria vesca 57918 TTG|GTATGAACAT...GTTGCTTTCTCA/TGCTTTCTCATT...CGTAG|GAC 2 1 8.84
78945631 GT-AG 0 1.000000099473604e-05 86 rna-XM_004287830.2 14698706 2 9231175 9231260 Fragaria vesca 57918 TCG|GTGAGTATCT...TGGCTGTTAATT/TGGCTGTTAATT...CACAG|GAT 0 1 88.889
78945632 GT-AG 0 0.000670194566785 132 rna-XM_004287830.2 14698706 3 9230991 9231122 Fragaria vesca 57918 GTG|GTATGTGTAT...AACTTCATAACA/TCTTGTTTGATT...CACAG|AGA 1 1 90.035
78945633 GT-AG 0 0.0024309173216735 84 rna-XM_004287830.2 14698706 4 9230824 9230907 Fragaria vesca 57918 GCG|GTATGATTAA...GAACTCTTATCG/AAGATAATAATT...TTCAG|GCA 0 1 91.865
78945634 GT-AG 0 0.1224675389766491 83 rna-XM_004287830.2 14698706 5 9230675 9230757 Fragaria vesca 57918 AAT|GTATATATTC...TTGTCGTTGATT/TTGTCGTTGATT...TGCAG|AGA 0 1 93.32
78945635 GT-AG 0 0.0031784640446984 103 rna-XM_004287830.2 14698706 6 9230482 9230584 Fragaria vesca 57918 TAT|GTAGGTTTTA...TTTTTCTTCATT/TTTTTCTTCATT...GGCAG|ATC 0 1 95.304
78945636 GT-AG 0 5.275140507116166e-05 153 rna-XM_004287830.2 14698706 7 9230152 9230304 Fragaria vesca 57918 AAG|GTGTGTTGTG...TTAACCTTAAAC/TCTGTTTTAACC...TACAG|GAA 0 1 99.206

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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]);