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 = 38490464

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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
213116661 GT-AG 0 1.000000099473604e-05 2078 rna-XM_020546910.3 38490464 1 277354508 277356585 Zea mays 4577 AAG|GTCAGTTATT...AAATTGTTGATT/TGATTATTTATT...TGCAG|TAT 0 1 18.318
213116662 GT-AG 0 1.000000099473604e-05 1659 rna-XM_020546910.3 38490464 2 277356819 277358477 Zea mays 4577 CAA|GTAAGTTAAC...TCATTATTAATT/TTTGTGCTCATT...ACTAG|GAC 2 1 24.423
213116663 GT-AG 0 1.000000099473604e-05 87 rna-XM_020546910.3 38490464 3 277358608 277358694 Zea mays 4577 CTG|GTGAGTCCAT...TTTACTTTATAT/AATTCTTTTATT...GCCAG|GAC 0 1 27.83
213116664 GT-AG 0 8.438731291738878e-05 85 rna-XM_020546910.3 38490464 4 277358764 277358848 Zea mays 4577 CAG|GTTTATTATA...ATATATTTGATC/ATATATTTGATC...TCCAG|GAT 0 1 29.638
213116665 GT-AG 0 1.2354078076878232e-05 483 rna-XM_020546910.3 38490464 5 277358993 277359475 Zea mays 4577 GTG|GTATTGAGCT...TATTCTGTGCCA/CATGTAGTGATG...TTCAG|ATG 0 1 33.412
213116666 GT-AG 0 1.000000099473604e-05 1901 rna-XM_020546910.3 38490464 6 277359578 277361478 Zea mays 4577 GAG|GTAAAATGTT...ATTTTCTTGCTT/ACATTAATCATT...TTTAG|ATT 0 1 36.085
213116667 GT-AG 0 0.0002343454616122 5597 rna-XM_020546910.3 38490464 7 277361754 277367350 Zea mays 4577 AAG|GTATGTATGC...GTATTTCTAACA/GTATTTCTAACA...CTAAG|GTC 2 1 43.291
213116668 GT-AG 0 9.795329516637546e-05 5168 rna-XM_020546910.3 38490464 8 277368969 277374136 Zea mays 4577 AAG|GTATGAAATT...TGCCCCTTAACA/GTTTTGGTCATA...AATAG|GTT 0 1 85.692

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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]);