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 = 7476852

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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
39173415 GT-AG 0 1.000000099473604e-05 2531 rna-gnl|WGS:WBNC|CERFAM_R09632_mrna 7476852 1 1482287 1484817 Certhia familiaris 73333 AAG|GTAAGAAAAT...TGTGTGTTAAAT/TGTGTGTTAAAT...TTCAG|GTT 0 1 19.133
39173416 GT-AG 0 5.703889874225183e-05 321 rna-gnl|WGS:WBNC|CERFAM_R09632_mrna 7476852 2 1484944 1485264 Certhia familiaris 73333 ACG|GTGTGCCTTT...AAATGCTTCACA/AAATGCTTCACA...AATAG|GTG 0 1 29.847
39173417 GT-AG 0 0.0091139741069919 1650 rna-gnl|WGS:WBNC|CERFAM_R09632_mrna 7476852 3 1485365 1487014 Certhia familiaris 73333 AAG|GTATGCATTT...ATTCCTTGGACT/TGGAATCTGATT...TACAG|TGA 1 1 38.35
39173418 GT-AG 0 0.0066936750325556 2486 rna-gnl|WGS:WBNC|CERFAM_R09632_mrna 7476852 4 1487164 1489649 Certhia familiaris 73333 AAG|GTACCTTAAC...GTCACTTTGTTA/CTTCCTGTCACT...AAGAG|GAA 0 1 51.02
39173419 GT-AG 0 0.0298342234571336 2726 rna-gnl|WGS:WBNC|CERFAM_R09632_mrna 7476852 5 1489718 1492443 Certhia familiaris 73333 TCA|GTTTACTGAG...CAATATTTAACT/CAATATTTAACT...GAAAG|TGT 2 1 56.803
39173420 GT-AG 0 0.0086895997985093 2706 rna-gnl|WGS:WBNC|CERFAM_R09632_mrna 7476852 7 1492570 1495275 Certhia familiaris 73333 AGT|GTTTGCAGTA...CTTTTTTTATCT/TCTTTTTTTATC...TTTAG|CTG 1 1 67.177

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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]);