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)

8 rows where transcript_id = 37556907

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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
207136139 GT-AG 0 0.0002148899986581 30924 rna-XM_026383165.1 37556907 1 7937332 7968255 Urocitellus parryii 9999 AAG|GTAGCGTGGG...TCCTCCTTGTTA/GAATATTTCATT...AACAG|TAC 0 1 5.249
207136140 GT-AG 0 1.000000099473604e-05 561 rna-XM_026383165.1 37556907 2 7936702 7937262 Urocitellus parryii 9999 AAG|GTAAGATAAT...TTAATTTTGAAA/TTGTAATTAATT...AATAG|GCA 0 1 11.602
207136141 GT-AG 0 1.000000099473604e-05 2445 rna-XM_026383165.1 37556907 3 7934148 7936592 Urocitellus parryii 9999 CAG|GTAAGAATAT...ACTGTATTAAAA/TAAGAATTAATT...TGCAG|CAC 1 1 21.639
207136142 GT-AG 0 1.000000099473604e-05 5421 rna-XM_026383165.1 37556907 4 7928652 7934072 Urocitellus parryii 9999 TTG|GTAAGAAATT...TTGACCTTTTTC/CAGATGTTGACC...TGCAG|ATG 1 1 28.545
207136143 GT-AG 0 1.000000099473604e-05 1075 rna-XM_026383165.1 37556907 5 7927314 7928388 Urocitellus parryii 9999 GTG|GTAAGTATGT...TTGTCTGTATTT/GAGCTTTTCAAC...TCCAG|ACT 0 1 52.762
207136144 GT-AG 0 1.000000099473604e-05 6760 rna-XM_026383165.1 37556907 6 7920445 7927204 Urocitellus parryii 9999 TTG|GTAAGAAGCT...AACTCTTTAATA/AATATACTAACT...TTTAG|GTT 1 1 62.799
207136145 GT-AG 0 1.000000099473604e-05 1638 rna-XM_026383165.1 37556907 7 7918758 7920395 Urocitellus parryii 9999 CAG|GTAAGTATTT...TATTACTTGATT/TATTACTTGATT...TCCAG|AAG 2 1 67.311
207136146 GT-AG 0 1.000000099473604e-05 2352 rna-XM_026383165.1 37556907 9 7914887 7917238 Urocitellus parryii 9999 GTG|GTGAGTAATC...GTGTTCTGATTT/TGTGTTCTGATT...CATAG|GTT 0 1 90.884

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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]);