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 = 25439132

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Suggested facets: dinucleotide_pair, score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
140324838 GT-AG 0 1.000000099473604e-05 1804 rna-XM_015765301.2 25439132 1 8373249 8375052 Oryza sativa 4530 GAG|GTTAGTGTGG...TATTCTTTAAGG/TGATTCTTCATT...GGCAG|GGC 1 1 0.707
140324839 GT-AG 0 0.0028309265199819 1799 rna-XM_015765301.2 25439132 2 8370985 8372783 Oryza sativa 4530 ATG|GTATGTTTGA...TATAATTTACCT/CTGTTACTCACA...ACCAG|CAT 1 1 10.383
140324840 GT-AG 0 1.000000099473604e-05 758 rna-XM_015765301.2 25439132 3 8369852 8370609 Oryza sativa 4530 CTG|GTAATGCTAA...TTTCTTTTAACA/TTTCTTTTAACA...TTCAG|CTC 1 1 18.186
140324841 GT-AG 0 3.794843563952534e-05 231 rna-XM_015765301.2 25439132 4 8369408 8369638 Oryza sativa 4530 CAC|GTACGTGCAG...GGAGCATTAATA/GCATTAATAATA...TGCAG|CCA 1 1 22.618
140324842 GT-AG 0 0.0001191643123982 162 rna-XM_015765301.2 25439132 5 8368874 8369035 Oryza sativa 4530 ATG|GTATGGCCAA...TACACCTTGACT/GAGTCTCTGACT...TTCAG|GTA 1 1 30.358
140324843 GT-AG 0 1.000000099473604e-05 79 rna-XM_015765301.2 25439132 6 8368551 8368629 Oryza sativa 4530 CGG|GTAAGCAGGT...TCTGCTTTTGCT/TTTTGCTTCATA...TTCAG|GTA 2 1 35.435
140324844 GT-AG 0 1.000000099473604e-05 559 rna-XM_015765301.2 25439132 7 8367844 8368402 Oryza sativa 4530 TGG|GTTAGATTTC...TCAATTTTGACT/TCAATTTTGACT...CGCAG|GCA 0 1 38.514
140324845 GC-GC 0 1.000000099473604e-05 617 rna-XM_015765301.2 25439132 8 8366865 8367481 Oryza sativa 4530 AGG|GCGGTAACAG...CTCGTCGTGGCG/TCGGTGCTCGCC...GCGGC|GGC 2 1 46.047

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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]);