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)

9 rows where transcript_id = 32765284

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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
183237097 GT-AG 0 1.000000099473604e-05 1253 rna-XM_004953037.2 32765284 1 30756082 30757334 Setaria italica 4555 GGG|GTAAGCACTA...TTGGTTTTGTTT/TGGGTACTGATT...ACCAG|GGC 1 1 25.926
183237098 GT-AG 0 1.000000099473604e-05 79 rna-XM_004953037.2 32765284 2 30755523 30755601 Setaria italica 4555 TAG|GTAAAGTAGA...TTGTGTTTACCT/TTTGTGTTTACC...TGCAG|GTG 1 1 35.588
183237099 GT-AG 0 1.000000099473604e-05 758 rna-XM_004953037.2 32765284 3 30754463 30755220 Setaria italica 4555 GAG|GTGAGATTTC...TCTTTTTTATTG/CTCTTTTTTATT...AGCAG|GTT 0 1 41.667
183237100 GT-AG 0 5.125204758348265e-05 83 rna-XM_004953037.2 32765284 4 30753693 30753775 Setaria italica 4555 AGG|GTAAGATTTA...TTTCCTTTAATT/TTTCCTTTAATT...CTCAG|TCA 0 1 55.495
183237101 GT-AG 0 0.0009797919973732 859 rna-XM_004953037.2 32765284 5 30752555 30753413 Setaria italica 4555 CCA|GTAAGTTTGC...TTTATTTTAATT/TTTATTTTAATT...TGCAG|GTT 0 1 61.111
183237102 GT-AG 0 0.0613836991570501 95 rna-XM_004953037.2 32765284 6 30752298 30752392 Setaria italica 4555 GCG|GTATGTTTAG...TTCTTCTTACTT/TTTGTTTTTATT...CTAAG|GTT 0 1 64.372
183237103 GT-AG 0 0.0050975610712442 88 rna-XM_004953037.2 32765284 7 30751274 30751361 Setaria italica 4555 AGG|GTATTTATCT...ATTTCCTCATTT/GATTTCCTCATT...TGTAG|TCT 0 1 83.213
183237104 GT-AG 0 1.000000099473604e-05 1456 rna-XM_004953037.2 32765284 8 30749602 30751057 Setaria italica 4555 AAG|GTAGAAGTTC...CCAATATTATTT/AAACAACTAATG...TCCAG|AAA 0 1 87.56
183237105 GT-AG 0 0.0004097376337839 566 rna-XM_004953037.2 32765284 9 30748775 30749340 Setaria italica 4555 CAC|GTTTTCCACC...GTTTACTGATCT/TGTTTACTGATC...TTCAG|CAA 0 1 92.814

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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]);