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 = 35543749

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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
199805421 GT-AG 0 1.000000099473604e-05 2201 rna-gnl|WGS:VXBI|TOXRED_R01473_mrna 35543749 1 15283 17483 Toxostoma redivivum 99882 GCT|GTGAGTGCCG...CTGGTTTTATCC/GCTGGTTTTATC...TGCAG|ATA 1 1 17.922
199805422 GT-AG 0 1.000000099473604e-05 278 rna-gnl|WGS:VXBI|TOXRED_R01473_mrna 35543749 2 14906 15183 Toxostoma redivivum 99882 TGG|GTCAGCAGCT...GATTCCTGATTT/TGATTCCTGATT...TGCAG|GGT 1 1 29.224
199805423 GT-AG 0 0.0042701409576667 317 rna-gnl|WGS:VXBI|TOXRED_R01473_mrna 35543749 3 14526 14842 Toxostoma redivivum 99882 CCC|GTATGTGGGG...TTTTCCCTGATC/TTTTCCCTGATC...TGCAG|CTC 1 1 36.416
199805424 GT-AG 0 1.000000099473604e-05 757 rna-gnl|WGS:VXBI|TOXRED_R01473_mrna 35543749 4 13644 14400 Toxostoma redivivum 99882 CCA|GTGAGTGAAA...CTTCCCTTACCC/CCTTCCCTTACC...TCCAG|ACC 0 1 50.685
199805425 GT-AG 0 1.000000099473604e-05 591 rna-gnl|WGS:VXBI|TOXRED_R01473_mrna 35543749 5 12905 13495 Toxostoma redivivum 99882 CAC|GTCAGTGATT...AGCTTCCTGACT/AGCTTCCTGACT...CCCAG|TGA 1 1 67.58
199805426 GT-AG 0 1.000000099473604e-05 940 rna-gnl|WGS:VXBI|TOXRED_R01473_mrna 35543749 6 11822 12761 Toxostoma redivivum 99882 ACG|GTAGGGCCAC...ATTTTTTTATTG/TATTTTTTTATT...GGCAG|GAT 0 1 83.904

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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]);