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 = 8855928

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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
47813440 GT-AG 0 0.0001963591677875 464 rna-XM_027263985.1 8855928 1 6102944 6103407 Coffea arabica 13443 TCA|GTGTGTATTT...TGATGTTTATCA/ATGATGTTTATC...ATTAG|GCT 1 1 4.071
47813441 GT-AG 0 1.000000099473604e-05 610 rna-XM_027263985.1 8855928 2 6100604 6101213 Coffea arabica 13443 CTG|GTAAGTGATT...TTTTTCTTCTAT/TTCTGGTTGACT...TGCAG|AAT 0 1 57.025
47813442 GT-AG 0 0.0002035313890079 82 rna-XM_027263985.1 8855928 3 6100243 6100324 Coffea arabica 13443 TTG|GTAATTTGCT...TTTGTTTTAATA/TTTGTTTTAATA...TGCAG|CTG 0 1 65.565
47813443 GT-AG 0 1.000000099473604e-05 80 rna-XM_027263985.1 8855928 4 6100135 6100214 Coffea arabica 13443 AAG|GTGGGGAATG...TTCTATTTGAAA/TTCTATTTGAAA...TGCAG|GAT 1 1 66.422
47813444 GT-AG 0 0.000119521994703 1311 rna-XM_027263985.1 8855928 5 6098190 6099500 Coffea arabica 13443 CAG|GTATGTGATA...ATGTTTTTAATG/ATGTTTTTAATG...TTCAG|GAG 2 1 85.828
47813445 GT-AG 0 1.000000099473604e-05 1173 rna-XM_027263985.1 8855928 6 6096872 6098044 Coffea arabica 13443 ATG|GTAAGTCCGT...AGGTTCATATCT/GTGCTTTTCAGT...TGCAG|GTA 0 1 90.266
47813446 GT-AG 0 0.0192554875297128 66 rna-XM_027263985.1 8855928 7 6096548 6096613 Coffea arabica 13443 ATG|GTATGTTGGT...TATCCCTTATTT/TGTATATTTATC...AACAG|AAG 0 1 98.163

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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]);