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)

7 rows where transcript_id = 15550491

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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
84004125 GT-AG 0 0.0002049837586703 490 rna-XM_028324945.1 15550491 1 56754367 56754856 Glycine soja 3848 CAG|GTATGGTTGC...CTTTCTTCAATA/TAGGAATTCATT...TGCAG|ATG 0 1 56.849
84004126 GT-AG 0 0.2073154047224508 131 rna-XM_028324945.1 15550491 2 56754106 56754236 Glycine soja 3848 AAT|GTATTCACTT...CTCTTTTTATAT/TTGGACTTCATT...CATAG|ATC 1 1 60.147
84004127 GT-AG 0 0.6989384177034678 306 rna-XM_028324945.1 15550491 3 56753711 56754016 Glycine soja 3848 GAG|GTACCTCTTA...GGATTCTTAATT/TTAATTATTACT...TACAG|CTT 0 1 62.405
84004128 GT-AG 0 2.4842697076000933e-05 594 rna-XM_028324945.1 15550491 4 56752878 56753471 Glycine soja 3848 TGG|GTAAGCACTA...TAATTCCTAATT/TTTCTATTCATT...TTCAG|ATC 2 1 68.468
84004129 GT-AG 0 1.000000099473604e-05 841 rna-XM_028324945.1 15550491 5 56751950 56752790 Glycine soja 3848 CAG|GTTCTAAGCC...ATCTTGTTAGTG/TAAGTATTTACT...CTTAG|GTT 2 1 70.675
84004130 GT-AG 0 0.0170128377816928 135 rna-XM_028324945.1 15550491 6 56751715 56751849 Glycine soja 3848 TCG|GTAAACATTG...TTGTTCTTAACT/TTGTTCTTAACT...GGAAG|ACA 0 1 73.212
84004131 GT-AG 0 2.2156271130703727e-05 83 rna-XM_028324945.1 15550491 7 56751424 56751506 Glycine soja 3848 CAG|GTGTTTATGT...ACTTCTTTATTT/TTAAGTTTTACT...TATAG|GTT 1 1 78.488

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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]);