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)

8 rows where transcript_id = 10143887

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Suggested facets: score, phase, in_cds

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
55681864 GT-AG 0 0.0002689933679437 371 rna-XM_023672364.1 10143887 1 7805192 7805562 Cucurbita pepo 3663 CAG|GTTTCAGTTT...TCATTCTTTTTT/AATCTGCTCATT...ATCAG|AAT 1 1 6.143
55681865 GT-AG 0 4.977872900443412e-05 208 rna-XM_023672364.1 10143887 2 7804940 7805147 Cucurbita pepo 3663 ACG|GTAAGTTTTC...AGTTTCTTATGG/ATCAGTCTAATT...CAAAG|GAT 0 1 7.163
55681866 GT-AG 0 0.0079256589227166 144 rna-XM_023672364.1 10143887 3 7804683 7804826 Cucurbita pepo 3663 CAG|GTAACTTTTG...GGCTCCTCAAAA/CTTGGGATTATT...TGCAG|GTC 2 1 9.782
55681867 GT-AG 0 1.0571221560962588e-05 127 rna-XM_023672364.1 10143887 4 7804366 7804492 Cucurbita pepo 3663 AGT|GTAGGGGTCT...GCTTTTTTGATA/GCTTTTTTGATA...TTCAG|GTC 0 1 14.186
55681868 GT-AG 0 3.946459836509099e-05 222 rna-XM_023672364.1 10143887 5 7803952 7804173 Cucurbita pepo 3663 CAG|GTACTTGTGC...ATCATCTTACTG/AATCATCTTACT...TGCAG|GGT 0 1 18.637
55681869 GT-AG 0 1.000000099473604e-05 398 rna-XM_023672364.1 10143887 6 7802792 7803189 Cucurbita pepo 3663 AAG|GTTCGTAATC...GAACCTTTAACC/ACCAGTCTCACT...AATAG|GAT 0 1 36.3
55681870 GT-AG 0 1.000000099473604e-05 524 rna-XM_023672364.1 10143887 7 7801699 7802222 Cucurbita pepo 3663 GGG|GTCAGTATAT...CAAATTTTGTTT/TGAAAACTGATA...TCCAG|GAC 2 1 49.49
55693037 GT-AG 0 4.880228523746009e-05 310 rna-XM_023672364.1 10143887 8 7800069 7800378 Cucurbita pepo 3663 CAG|GTACGTACGC...ATTCTCTTATTA/GATTTTCTCAAT...TCTAG|ATT   0 80.088

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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]);