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)

5 rows where transcript_id = 38490422

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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
213116223 GT-AG 0 0.0077391962053482 622 rna-XM_008663729.4 38490422 2 175113139 175113760 Zea mays 4577 CCG|GTAAACTTTC...ATTTACTTAAAA/CAGTGTTTAATA...CACAG|ATA 1 1 9.089
213116224 GT-AG 0 0.0004989867666899 89 rna-XM_008663729.4 38490422 3 175112702 175112790 Zea mays 4577 AAG|GTATGCCCGT...AATATCCTGATA/AATATCCTGATA...CACAG|AGG 1 1 15.965
213116225 GT-AG 0 6.959515230337481e-05 91 rna-XM_008663729.4 38490422 4 175111289 175111379 Zea mays 4577 GAG|GTATGATGCT...GATCCCTGGATA/TGTAAATTGATC...GTCAG|GTG 0 1 42.087
213116226 GT-AG 0 0.0464608095400985 93 rna-XM_008663729.4 38490422 5 175109429 175109521 Zea mays 4577 GAG|GTATACATAT...GTTTCCTTACTC/TGTTTCCTTACT...GGCAG|GAG 0 1 77.001
213136389 GT-AG 0 1.450808592803854e-05 1466 rna-XM_008663729.4 38490422 1 175113990 175115455 Zea mays 4577 ATC|GTAAGTCCGT...CTAGTTTTGAAA/CTAGTTTTGAAA...TGCAG|GTA   0 7.113

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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]);