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 = 28837506

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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
160841325 GT-AG 0 1.000000099473604e-05 96 rna-XM_011027419.1 28837506 2 7673904 7673999 Populus euphratica 75702 AAG|GTAAGTTCCT...TTTTTCTTTTTC/AATCATATAAAT...TTCAG|AGA 0 1 6.456
160841326 GT-AG 0 0.0001058634691949 104 rna-XM_011027419.1 28837506 3 7674496 7674599 Populus euphratica 75702 CTG|GTAATCATCA...TAGGCTCTAATT/TAGGCTCTAATT...TACAG|TTT 1 1 26.594
160841327 GT-AG 0 1.0121974506145769e-05 871 rna-XM_011027419.1 28837506 4 7674654 7675524 Populus euphratica 75702 AAT|GTAAGATACC...CATGCCTTACTG/TCATGCCTTACT...TGCAG|ATG 1 1 28.786
160841328 GT-AG 0 1.000000099473604e-05 112 rna-XM_011027419.1 28837506 5 7675786 7675897 Populus euphratica 75702 CAG|GTGATTATTG...AACCTCTTATTC/TTCTTGTTTATT...AACAG|GCT 1 1 39.383
160841329 GT-AG 0 0.0048134307517387 1893 rna-XM_011027419.1 28837506 6 7675951 7677843 Populus euphratica 75702 CAG|GTATATATAC...CATGCCTTATTC/TGAGATTTCATT...TGCAG|ATA 0 1 41.535
160841330 GT-AG 0 1.000000099473604e-05 182 rna-XM_011027419.1 28837506 7 7677968 7678149 Populus euphratica 75702 CGG|GTAGGTGCCT...CAAGTTTTGACT/TTTTGACTGACC...TCCAG|GTA 1 1 46.569
160841331 GT-AG 0 3.802022330325174e-05 833 rna-XM_011027419.1 28837506 8 7678405 7679237 Populus euphratica 75702 CAG|GTATGACTCT...CCTTGCTTATTT/TGAAATTTCATT...AACAG|GTT 1 1 56.922

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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]);