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 = 25340384

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Suggested facets: score, phase, in_cds

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
139664838 GT-AG 0 1.000000099473604e-05 9449 rna-XM_007943818.1 25340384 2 4558659 4568107 Orycteropus afer 9818 GAG|GTAAAAATCT...ATTTTTTTAAAA/ATTTTTTTAAAA...TGAAG|CTC 0 1 58.09
139664839 GT-AG 0 1.8076927913809606e-05 2046 rna-XM_007943818.1 25340384 3 4556479 4558524 Orycteropus afer 9818 CAA|GTAAGTGTGT...TTTTCTTTACCT/TTTTTCTTTACC...CTTAG|GTC 2 1 66.797
139664840 GT-AG 0 0.0015628988453835 33810 rna-XM_007943818.1 25340384 4 4522617 4556426 Orycteropus afer 9818 GAG|GTATGATTAT...TATTCTTTGACC/AAATGACTTATT...CATAG|GAT 0 1 70.175
139664841 GT-AG 0 0.000145577144445 1607 rna-XM_007943818.1 25340384 5 4520920 4522526 Orycteropus afer 9818 CAG|GTAACGTGAA...TTTGCTTTACTT/TAGTTACTGATT...ACTAG|CAG 0 1 76.023
139664842 GT-AG 0 0.0001179873996044 2476 rna-XM_007943818.1 25340384 6 4518281 4520756 Orycteropus afer 9818 AAG|GTACATCTTT...TGTTTCTTTTTT/ATATCACTCATA...ATCAG|GAG 1 1 86.615
139664843 GT-AG 0 1.000000099473604e-05 3446 rna-XM_007943818.1 25340384 7 4514718 4518163 Orycteropus afer 9818 CAG|GTGAGAATGT...AATTCATTGATT/CTTCAATTCATT...TGCAG|AGA 1 1 94.217
139665247 GT-AG 0 0.0002624241350378 9965 rna-XM_007943818.1 25340384 1 4568946 4578910 Orycteropus afer 9818 CGA|GTACGTACCA...ATTTCCTTTCTT/AATGTTATAAAT...TGCAG|ATT   0 4.873

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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]);