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)

8 rows where transcript_id = 4181791

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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
21587254 GT-AG 0 1.000000099473604e-05 887 rna-XM_010670532.2 4181791 1 3582358 3583244 Beta vulgaris 161934 CAG|GTGAAGTTAC...TCCTCCTTAATA/GTCATTTTGATA...TACAG|GTT 0 1 5.552
21587255 GT-AG 0 1.000000099473604e-05 924 rna-XM_010670532.2 4181791 2 3581245 3582168 Beta vulgaris 161934 GAA|GTGAGTTATT...TTATTTTTATAA/ATATATTTAACT...TACAG|GTG 0 1 10.094
21587256 GT-AG 0 1.000000099473604e-05 95 rna-XM_010670532.2 4181791 3 3581057 3581151 Beta vulgaris 161934 GAG|GTGATGTTTT...CTTTCCTAAATG/ACTTTCCTAAAT...TGCAG|ATT 0 1 12.329
21587257 GT-AG 0 1.000000099473604e-05 80 rna-XM_010670532.2 4181791 4 3580794 3580873 Beta vulgaris 161934 GAG|GTGCTTTACA...GTTGTGTTAGAT/TGCCGACTAATA...TCCAG|GTT 0 1 16.727
21587258 GT-AG 0 0.0026818465925075 92 rna-XM_010670532.2 4181791 5 3580599 3580690 Beta vulgaris 161934 CTG|GTATGCGTCC...TCTATTTTATAT/TTTATATTCAAT...TACAG|CGG 1 1 19.202
21587259 GT-AG 0 0.0002102725693945 879 rna-XM_010670532.2 4181791 6 3579534 3580412 Beta vulgaris 161934 AAG|GTACTCAATT...TTTTTGTTGATG/TTTTTGTTGATG...TGCAG|GAA 1 1 23.672
21587260 GT-AG 0 1.000000099473604e-05 1869 rna-XM_010670532.2 4181791 7 3575203 3577071 Beta vulgaris 161934 CCT|GTAAGGCCAT...TTGTTTTTATTA/CTTGTTTTTATT...TTCAG|AAG 0 1 82.841
21587261 GT-AG 0 1.000000099473604e-05 189 rna-XM_010670532.2 4181791 8 3574442 3574630 Beta vulgaris 161934 AAG|GTGAATCTTT...TATTCTTTGGTT/GAGGATTTGATT...GCCAG|ATC 2 1 96.587

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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]);