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 = 25413750

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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
140208493 GT-AG 0 1.000000099473604e-05 1106 rna-XM_006646069.3 25413750 1 18881019 18882124 Oryza brachyantha 4533 GAG|GTACGAATTC...TACATGTTACTT/TTCGAACTTACG...TACAG|ATC 2 1 9.267
140208494 GT-AG 0 1.000000099473604e-05 108 rna-XM_006646069.3 25413750 2 18877736 18877843 Oryza brachyantha 4533 CAG|GTAGGTGATG...GTACCTTTAAGT/TAGTATCTCATC...TGCAG|GAT 0 1 87.316
140208495 GT-AG 0 0.0022569063249417 135 rna-XM_006646069.3 25413750 3 18877525 18877659 Oryza brachyantha 4533 AAG|GTATTCGTAA...ATTTCTTCAGCG/AGTTTATTTATT...CACAG|TAG 1 1 89.184
140208496 GT-AG 0 0.3838019913416978 86 rna-XM_006646069.3 25413750 4 18877368 18877453 Oryza brachyantha 4533 GCG|GTATACTGAA...ATTTTTTTAACA/ATTTTTTTAACA...TTCAG|GCC 0 1 90.929
140208497 GT-AG 0 1.000000099473604e-05 87 rna-XM_006646069.3 25413750 5 18877215 18877301 Oryza brachyantha 4533 CAT|GTAATGCATC...CTCTTCTAAATC/TCTCTTCTAAAT...TACAG|AGA 0 1 92.552
140208498 GT-AG 0 0.0001261603294293 575 rna-XM_006646069.3 25413750 6 18876550 18877124 Oryza brachyantha 4533 TAT|GTAAATATTT...CTCATCTGAACC/AGTTAACTCATC...GGCAG|ATC 0 1 94.764
140208499 GT-AG 0 0.0004836390205355 1215 rna-XM_006646069.3 25413750 7 18875158 18876372 Oryza brachyantha 4533 AAG|GTACATTATT...ATTTACTTAATA/TATTTACTTAAT...TGCAG|GAG 0 1 99.115

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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]);