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)

7 rows where transcript_id = 38341171

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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
211992426 GT-AG 0 3.620689470225663e-05 892 rna-XM_028018000.1 38341171 2 11369452 11370343 Xiphophorus couchianus 32473 AGG|GTATGACACT...GTCTTCATAATT/GATGTCTTCATA...ACTAG|AAC 2 1 55.491
211992427 GT-AG 0 1.000000099473604e-05 542 rna-XM_028018000.1 38341171 3 11370567 11371108 Xiphophorus couchianus 32473 CAG|GTACAGAAGT...TTATCCTTTTCT/TCTACATTTACT...TTCAG|CTG 0 1 61.66
211992428 GT-AG 0 1.000000099473604e-05 172 rna-XM_028018000.1 38341171 4 11371302 11371473 Xiphophorus couchianus 32473 CTG|GTGATCAGCT...TTTTTCTTTTTT/TACAATTTGAAA...TGTAG|GTG 1 1 66.999
211992429 GT-AG 0 0.3770558013829898 168 rna-XM_028018000.1 38341171 5 11371641 11371808 Xiphophorus couchianus 32473 AAG|GTATTTTTCA...TTTGTCTTAACG/TTTGTCTTAACG...CCAAG|GAA 0 1 71.618
211992430 GT-AG 0 1.000000099473604e-05 130 rna-XM_028018000.1 38341171 6 11372083 11372212 Xiphophorus couchianus 32473 AAG|GTGGGACAGC...TTGATGTTAATA/TTGATGTTAATA...TTCAG|GTG 1 1 79.198
211992431 GT-AG 0 1.5593324498424528e-05 409 rna-XM_028018000.1 38341171 7 11372431 11372839 Xiphophorus couchianus 32473 CAG|GTAAGCCTTT...TGAACTTTACAA/ATGAACTTTACA...AACAG|GCA 0 1 85.228
211997984 GT-AG 0 1.000000099473604e-05 744 rna-XM_028018000.1 38341171 1 11366930 11367673 Xiphophorus couchianus 32473 GCG|GTCAGTTCAT...GTTTTTTTCTCC/GAAGTTCTAAAA...CGCAG|TGG   0 8.299

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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]);