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 = 10378423

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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
57022532 GT-AG 0 0.0010873737413845 2063 rna-XM_025138133.1 10378423 1 6418532 6420594 Cynara cardunculus 4265 CAG|GTAACCTAGC...TTCTTGTTAAGC/GATTTGCTCACT...TCCAG|GTC 0 1 3.383
57022533 GT-AG 0 1.000000099473604e-05 117 rna-XM_025138133.1 10378423 2 6420793 6420909 Cynara cardunculus 4265 ATG|GTACGATCCA...TGGTCTATGATT/ATTCCACTAATA...GGCAG|GGA 0 1 8.346
57022534 GT-AG 0 1.000000099473604e-05 1013 rna-XM_025138133.1 10378423 3 6421033 6422045 Cynara cardunculus 4265 CAG|GTTAGTCATC...ATTTTTTTATAA/CATTTTTTTATA...TGCAG|GTG 0 1 11.429
57022535 GT-AG 0 0.0001674273937231 88 rna-XM_025138133.1 10378423 4 6422084 6422171 Cynara cardunculus 4265 GAG|GTTTTTTCTT...TAGGTTCTAACT/TAGGTTCTAACT...GACAG|ATG 2 1 12.381
57022536 GT-AG 0 0.0032546242876439 625 rna-XM_025138133.1 10378423 5 6422329 6422953 Cynara cardunculus 4265 AGG|GTACTTTCTT...AACACCTTATTT/CTGTATCTAATA...CACAG|GAT 0 1 16.316
57022537 GT-AG 0 2.8280623625019646e-05 179 rna-XM_025138133.1 10378423 6 6424605 6424783 Cynara cardunculus 4265 AAA|GTAAGTACCT...TAGTTTTTGACA/TAGTTTTTGACA...TACAG|ATT 1 1 57.694
57022538 GT-AG 0 1.1664723448901653e-05 56 rna-XM_025138133.1 10378423 7 6426429 6426484 Cynara cardunculus 4265 GAA|GTATGAGAAT...GAAGCCTCATTA/GGAAGCCTCATT...TGAAG|AAT 2 1 98.922

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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]);