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 = 3395305

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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
16698553 GT-AG 0 0.0003088394375205 620 rna-gnl|WGS:VXAK|AREINT_R13940_mrna 3395305 1 566183 566802 Arenaria interpres 54971 CAG|GTATTTCAAT...GACTCTTCAACT/TGACTCTTCAAC...TCCAG|TTC 1 1 9.08
16698554 GT-AG 0 1.8729838724178247e-05 834 rna-gnl|WGS:VXAK|AREINT_R13940_mrna 3395305 2 565285 566118 Arenaria interpres 54971 CCG|GTATGAACAC...AAGGACTTAATC/TCTCTTGTAATC...GCCAG|TTT 2 1 17.04
16698555 GT-AG 0 1.000000099473604e-05 556 rna-gnl|WGS:VXAK|AREINT_R13940_mrna 3395305 3 564633 565188 Arenaria interpres 54971 AAG|GTACTGAATC...CTGGCTTTGGTT/GTGATACTGAAA...CTCAG|ATT 2 1 28.98
16698556 GT-AG 0 1.000000099473604e-05 340 rna-gnl|WGS:VXAK|AREINT_R13940_mrna 3395305 4 564100 564439 Arenaria interpres 54971 AAG|GTGAGATGGC...GTGCCCTAAGTA/CGTGCCCTAAGT...TGCAG|ACG 0 1 52.985
16698557 GT-AG 0 0.0005818412189535 1457 rna-gnl|WGS:VXAK|AREINT_R13940_mrna 3395305 5 562514 563970 Arenaria interpres 54971 AGG|GTATGATACC...AAATCCTAAACA/ATGAGTCTGAAA...CCCAG|AGA 0 1 69.03
16698558 GT-AG 0 1.000000099473604e-05 347 rna-gnl|WGS:VXAK|AREINT_R13940_mrna 3395305 6 562020 562366 Arenaria interpres 54971 GAG|GTAGGAAATG...TAATCTATAACT/TAATCTATAACT...TGCAG|CTC 0 1 87.313

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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]);