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)

6 rows where transcript_id = 12720296

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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
67622851 GT-AG 0 6.540995527083506e-05 1615 rna-XM_009911618.1 12720296 1 1604125 1605739 Dryobates pubescens 118200 CGG|GTACGCAGGA...TTCCTCTTGGTC/TAGTTGTTCAGA...TTTAG|TTT 0 1 11.028
67622852 GT-AG 0 0.0001832709610657 931 rna-XM_009911618.1 12720296 2 1605921 1606851 Dryobates pubescens 118200 GAG|GTACACAGTT...TTCTCTTTTGTT/TTTTGTTTTATT...TAAAG|GCA 1 1 26.149
67622853 GT-AG 0 1.000000099473604e-05 599 rna-XM_009911618.1 12720296 3 1606957 1607555 Dryobates pubescens 118200 AAG|GTAAAAAAGC...TCAGATTTAACT/TCAGATTTAACT...CAAAG|GTT 1 1 34.921
67622854 GT-AG 0 1.000000099473604e-05 79 rna-XM_009911618.1 12720296 4 1607784 1607862 Dryobates pubescens 118200 AAG|GTAAGACCTA...TAGTCTATAGTT/TCCTTAATCATA...TCCAG|GTA 1 1 53.968
67622855 GT-AG 0 2.1650038652827932e-05 538 rna-XM_009911618.1 12720296 5 1608094 1608631 Dryobates pubescens 118200 CAG|GTAGGTTTTC...GCTTACTTAAAG/TACAAGCTTACT...TGTAG|GTG 1 1 73.266
67622856 GT-AG 0 1.000000099473604e-05 112 rna-XM_009911618.1 12720296 6 1608733 1608844 Dryobates pubescens 118200 TTG|GTAAGTTAAC...ACAACCCTACCC/CCATGAGTAATA...TGTAG|GTC 0 1 81.704

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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]);