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 = 30863705

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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
172492031 GT-AG 0 0.280766525691298 88 rna-XM_025312238.1 30863705 1 727650 727737 Rhizophagus irregularis 588596 CAA|GTATATTTTG...ATAACTTTACTG/ATGTTTATAACT...AATAG|AGA 2 1 4.796
172492032 GT-AG 0 1.0550045351256122e-05 85 rna-XM_025312238.1 30863705 2 727965 728049 Rhizophagus irregularis 588596 CCG|GTAAGTCTAC...TTTTTTTTAAAA/TTTTTTTTTAAA...ATTAG|GAT 1 1 15.575
172492033 GT-AG 0 0.0005153203575341 83 rna-XM_025312238.1 30863705 3 729182 729264 Rhizophagus irregularis 588596 AAA|GTATGAATTT...TGTTTATTAATA/TATTTGTTTATT...TATAG|TTC 2 1 69.326
172492034 GT-AG 0 0.0007681812378813 69 rna-XM_025312238.1 30863705 4 729415 729483 Rhizophagus irregularis 588596 AAT|GTAAGTTTCG...TTATTTTTATTG/CTTATTTTTATT...TTTAG|TTC 2 1 76.448
172492035 GT-AG 0 1.000000099473604e-05 71 rna-XM_025312238.1 30863705 5 729560 729630 Rhizophagus irregularis 588596 GAT|GTGAGTAACA...AATGTCCTGATA/AATGTCCTGATA...TTTAG|GTT 0 1 80.057
172492036 GT-AG 0 0.0006684235583094 80 rna-XM_025312238.1 30863705 6 729795 729874 Rhizophagus irregularis 588596 TGA|GTAAGCCTTC...CAATTATTAATT/TGTTTATTTATC...CATAG|TTT 2 1 87.844

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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]);