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)

10 rows where transcript_id = 33469734

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Suggested facets: score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
187538782 GT-AG 0 1.0371529100984662e-05 1298 rna-XM_002465406.2 33469734 1 69686981 69688278 Sorghum bicolor 4558 GAG|GTAAGCTGAT...GCCCTCTTACAT/CATTTTTTCATC...TGCAG|CAT 0 1 9.689
187538783 GT-AG 0 1.000000099473604e-05 74 rna-XM_002465406.2 33469734 2 69688334 69688407 Sorghum bicolor 4558 TAG|GTAAGTAACT...AATTCCTGATTA/GCAGTTCTCACT...TGCAG|AGG 1 1 10.985
187538784 GT-AG 0 2.077445022375083e-05 102 rna-XM_002465406.2 33469734 3 69688584 69688685 Sorghum bicolor 4558 AAA|GTAAGCCTAA...TGAACCTCATCA/GTGAACCTCATC...TGTAG|GTT 0 1 15.134
187538785 GT-AG 0 1.000000099473604e-05 229 rna-XM_002465406.2 33469734 4 69688887 69689115 Sorghum bicolor 4558 CAG|GTGTTACCTT...GTGACTTTTGCA/CTGGTTCTAATG...TACAG|GCC 0 1 19.873
187538786 GT-AG 0 0.0024928071723766 89 rna-XM_002465406.2 33469734 5 69689376 69689464 Sorghum bicolor 4558 CCT|GTAAGCAATT...ATATCCTTATCT/TATATCCTTATC...TGTAG|TGG 2 1 26.002
187538787 GT-AG 0 1.000000099473604e-05 77 rna-XM_002465406.2 33469734 6 69689776 69689852 Sorghum bicolor 4558 TAG|GTAATAGCAC...CTACTCATATTT/AGGCTACTCATA...TTCAG|GTG 1 1 33.333
187538788 GT-AG 0 1.000000099473604e-05 88 rna-XM_002465406.2 33469734 7 69690074 69690161 Sorghum bicolor 4558 CAG|GTAAAGGAGG...TCACTTTTAGAA/CTGGTACTCACT...TGTAG|GTT 0 1 38.543
187538789 GT-AG 0 1.000000099473604e-05 450 rna-XM_002465406.2 33469734 8 69690503 69690952 Sorghum bicolor 4558 AAG|GTAAAGCCTT...ACTACCTTATCT/TATGATTTGATT...GACAG|GAT 2 1 46.582
187538790 GT-AG 0 1.000000099473604e-05 104 rna-XM_002465406.2 33469734 9 69691747 69691850 Sorghum bicolor 4558 CAG|GTAATTGCAA...TTTACCTTATTA/TTAATTCTTATT...GACAG|CAA 1 1 65.299
187538791 GT-AG 0 1.000000099473604e-05 608 rna-XM_002465406.2 33469734 10 69692093 69692700 Sorghum bicolor 4558 CAG|GTAATAAAGT...AAATCTCTAATG/ATGGGTCTAATA...TGCAG|AAA 0 1 71.004

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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]);