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 = 8855921

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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
47813375 GT-AG 0 1.000000099473604e-05 1191 rna-XM_027264467.1 8855921 1 7661452 7662642 Coffea arabica 13443 GAG|GTAAGTGTAA...ATATTTTTGCCA/TGTTTGGTCATT...TTCAG|GTA 0 1 0.18
47813376 GT-AG 0 0.6082793529799022 451 rna-XM_027264467.1 8855921 2 7662827 7663277 Coffea arabica 13443 TAC|GTATCTGCTG...TGATGTTTATCA/ATGATGTTTATC...ATTAG|GCT 1 1 5.711
47813377 GT-AG 0 1.000000099473604e-05 610 rna-XM_027264467.1 8855921 3 7665008 7665617 Coffea arabica 13443 CTG|GTAAGTGATT...TTTTTCTTCTAT/CTTGTACTGAAG...TGCAG|AAT 0 1 57.71
47813378 GT-AG 0 2.326278909981532e-05 84 rna-XM_027264467.1 8855921 4 7665897 7665980 Coffea arabica 13443 TTG|GTAATTTGCT...TTGTTTCTAATA/TTGTTTCTAATA...TGCAG|CTG 0 1 66.096
47813379 GT-AG 0 1.000000099473604e-05 80 rna-XM_027264467.1 8855921 5 7666009 7666088 Coffea arabica 13443 AAG|GTGGGGAATG...TTCTATTTGAAA/TTCTATTTGAAA...TGCAG|GAT 1 1 66.937
47813380 GT-AG 0 7.140887019425005e-05 1311 rna-XM_027264467.1 8855921 6 7666723 7668033 Coffea arabica 13443 CAG|GTATGTGATA...TTATTTTTGAAC/TTATTTTTGAAC...TTCAG|GAG 2 1 85.993
47813381 GT-AG 0 1.000000099473604e-05 1619 rna-XM_027264467.1 8855921 7 7668179 7669797 Coffea arabica 13443 ATG|GTAAGTCCGT...AGGTTCATATCT/GTGCTTTTCAGT...TGCAG|GTA 0 1 90.352

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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]);