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 = 37986734

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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
209726862 GT-AG 0 0.002288108026519 83 rna-XM_047296983.1 37986734 2 56800 56882 Vigna umbellata 87088 CAG|GTCTCATACT...GTTAACTTAATT/TTCTCTCTCATC...ACCAG|TGC 0 1 18.598
209726863 GT-AG 0 0.0003493136616913 78 rna-XM_047296983.1 37986734 3 56586 56663 Vigna umbellata 87088 AGA|GTAAATTCGT...ACGGCGTTAACT/ACGGCGTTAACT...TACAG|ATT 1 1 28.036
209726864 GT-AG 0 0.000706932307955 612 rna-XM_047296983.1 37986734 4 55872 56483 Vigna umbellata 87088 AGG|GTCTGTTCTG...TATGCTTTAAAA/TTGATTTTTATA...TGCAG|CGG 1 1 35.115
209726865 GT-AG 0 0.0637722823140816 254 rna-XM_047296983.1 37986734 5 55493 55746 Vigna umbellata 87088 CAA|GTATTCCCTT...ATCTTCTGAATG/AATCTTCTGAAT...GATAG|ACG 0 1 43.789
209726866 GT-AG 0 1.98242712022186e-05 78 rna-XM_047296983.1 37986734 6 55128 55205 Vigna umbellata 87088 AAA|GTACTAAATT...GTGCCTTTCATT/GTGCCTTTCATT...TTCAG|ATT 2 1 63.706
209726867 GT-AG 0 1.000000099473604e-05 371 rna-XM_047296983.1 37986734 7 54672 55042 Vigna umbellata 87088 ATG|GTAGTTACAT...CATTGCTTATTG/CCATTGCTTATT...GGCAG|CTA 0 1 69.604
209726869 GT-AG 0 1.7907477254836226e-05 794 rna-XM_047296983.1 37986734 1 57025 57818 Vigna umbellata 87088 GGA|GTAAGGCTCT...TTTTTTTTATTT/ATTTTTTTTATT...AAAAG|AAG   0 10.687

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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]);