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 = 30001186

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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
168077804 GT-AG 0 0.1148395158019071 101 rna-XM_009371558.2 30001186 1 1643443 1643543 Pyrus x bretschneideri 225117 TAG|GTACCTTATT...TTTTTCTTTTTT/AGTGAATTGATT...TTCAG|CTC 1 1 51.352
168077805 GT-AG 0 0.0002787239778213 127 rna-XM_009371558.2 30001186 2 1643193 1643319 Pyrus x bretschneideri 225117 AAG|GTATGCGAAA...AATTTTTTATAC/AAATTTTTTATA...AACAG|GGA 1 1 56.245
168077806 GT-AG 0 0.0001687312502101 209 rna-XM_009371558.2 30001186 3 1642778 1642986 Pyrus x bretschneideri 225117 AAG|GTACTTTCCC...CGAGTCTTCACT/CGAGTCTTCACT...TTCAG|GGA 0 1 64.439
168077807 GT-AG 0 0.004575617069965 80 rna-XM_009371558.2 30001186 4 1642487 1642566 Pyrus x bretschneideri 225117 TTG|GTATGCAATC...GAAGCTTTTATG/TTGTAGCTAATA...TTCAG|ATA 1 1 72.832
168077808 GT-AG 0 0.0002100864818107 75 rna-XM_009371558.2 30001186 5 1642174 1642248 Pyrus x bretschneideri 225117 CTA|GTAATTGTCT...TGTTTTTTAATA/TGTTTTTTAATA...TGCAG|CGG 2 1 82.299
168077809 GT-AG 0 3.2646497927000865e-05 85 rna-XM_009371558.2 30001186 6 1641941 1642025 Pyrus x bretschneideri 225117 CTT|GTAAGTAAAC...TGACTCTTGAAT/TGACTCTTGAAT...TTCAG|ATA 0 1 88.186

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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]);