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)

5 rows where transcript_id = 28932406

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Suggested facets: score, in_cds

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
161301384 GT-AG 0 0.0001008657501719 3579 rna-XM_002299886.3 28932406 1 27097865 27101443 Populus trichocarpa 3694 CAG|GTAATCTCTC...ATGCTCTAAATA/AATATTCTAATT...TGCAG|ACT 2 1 1.577
161317247 GT-AG 0 0.0058851460371181 1869 rna-XM_002299886.3 28932406 2 27091721 27093589 Populus trichocarpa 3694 CAG|GTACCATTCT...TTTTTTTTTTTA/ATCATTCTAAGA...TGAAG|GCT   0 79.96
161317248 GT-AG 0 1.000000099473604e-05 268 rna-XM_002299886.3 28932406 3 27091360 27091627 Populus trichocarpa 3694 CAG|GTAAATGGAA...TTCCTGTTATTA/TGCCTTCTGATC...TGTAG|GGT   0 81.665
161317249 GT-AG 0 1.000000099473604e-05 479 rna-XM_002299886.3 28932406 4 27090272 27090750 Populus trichocarpa 3694 AAG|GTCAGTTGGA...TTCTCTCTAATG/TTCTCTCTAATG...TGCAG|GCC   0 92.831
161317250 GT-AG 0 1.1036930899433847e-05 120 rna-XM_002299886.3 28932406 5 27089992 27090111 Populus trichocarpa 3694 TAG|GTAGGTTCAT...GAATGCTTATTT/TGAATGCTTATT...TCCAG|TTT   0 95.765

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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]);