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)

8 rows where transcript_id = 7738627

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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
40790453 GT-AG 0 1.000000099473604e-05 7574 rna-XM_009895454.1 7738627 1 42166 49739 Charadrius vociferus 50402 CGG|GTGAGCGGCT...CCCCCCTCACCT/GCCCCCCTCACC...CGCAG|ACG 0 1 11.488
40790454 GT-AG 0 1.000000099473604e-05 540 rna-XM_009895454.1 7738627 3 49917 50456 Charadrius vociferus 50402 AAC|GTGAGCAGGG...GTGGCATTGAGC/GTGGCATTGAGC...CACAG|CTA 2 1 22.536
40790455 GT-AG 0 1.000000099473604e-05 104 rna-XM_009895454.1 7738627 4 50678 50781 Charadrius vociferus 50402 TAG|GTGGGGTCCT...GGTGCCCTGGCG/GCGGTGCTGAGC...CCCAG|GCA 1 1 36.409
40790456 GT-AG 0 1.000000099473604e-05 650 rna-XM_009895454.1 7738627 5 50940 51589 Charadrius vociferus 50402 TCG|GTGAGCGGCC...ATGCCCGTCGCC/GAGGTACTGATG...CCCAG|GGC 0 1 46.328
40790457 GT-AG 0 1.000000099473604e-05 76 rna-XM_009895454.1 7738627 6 51679 51754 Charadrius vociferus 50402 GAG|GTGGGGGGCA...CCCTCCTGGCCC/CCCGTGCTGAGC...CACAG|GTA 2 1 51.915
40790458 GT-AG 0 1.000000099473604e-05 558 rna-XM_009895454.1 7738627 7 51979 52536 Charadrius vociferus 50402 TGG|GTGCAGGGAT...CTGGCCGTGCTC/GCCGTGCTCACA...CACAG|CTG 1 1 65.976
40790459 GT-AG 0 1.000000099473604e-05 105 rna-XM_009895454.1 7738627 9 54924 55028 Charadrius vociferus 50402 AAG|GTGAGGTGGG...GTGTCCTGAACC/CGTGTCCTGAAC...CCCAG|CAG 1 1 80.289
40790460 GT-AG 0 1.000000099473604e-05 97 rna-XM_009895454.1 7738627 10 55131 55227 Charadrius vociferus 50402 AGG|GTGAGCAGCG...GGTGCTGGAGCT/CGGTGCTGGAGC...GGCAG|AGC 1 1 86.692

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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]);