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 = 34009247

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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
190420410 GT-AG 0 0.0001018650365197 25057 rna-XM_035358484.1 34009247 1 217432 242488 Stegodyphus dumicola 202533 TCA|GTAAGTTAAT...TTTTTTTTCGTT/TTTTTTTTCGTT...TTTAG|TTG 1 1 18.043
190420411 GT-AG 0 1.73819895603326e-05 136705 rna-XM_035358484.1 34009247 2 80674 217378 Stegodyphus dumicola 202533 ATG|GTAAGTTATG...GACATCTTAGTC/ATTTTTTTGAAG...TTCAG|GTT 0 1 26.147
190420412 GT-AG 0 1.000000099473604e-05 5663 rna-XM_035358484.1 34009247 3 74938 80600 Stegodyphus dumicola 202533 AAG|GTAAGTTAAA...TATTCCTTTCTT/TATTTAATTACA...TTCAG|ATG 1 1 37.309
190420413 GT-AG 0 2.166583887636249e-05 1722 rna-XM_035358484.1 34009247 4 73002 74723 Stegodyphus dumicola 202533 CAA|GTAAGTATTT...TTCGTTTTATAT/CTTCGTTTTATA...CATAG|GCT 2 1 70.031
190420414 GT-AG 0 1.2833160760055852e-05 12257 rna-XM_035358484.1 34009247 5 60596 72852 Stegodyphus dumicola 202533 AAG|GTAAGTTATA...TTTTTTTTATAT/ATTTTTTTTATA...CCCAG|AGA 1 1 92.813

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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]);