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 = 37986797

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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
209727189 GT-AG 0 0.0421267986508128 95 rna-XM_047306398.1 37986797 1 12995 13089 Vigna umbellata 87088 CAA|GTACGCATTT...TTGATCTTAATT/TTGATCTTAATT...TTCAG|AAA 1 1 31.68
209727190 GT-AG 0 1.000000099473604e-05 117 rna-XM_047306398.1 37986797 2 13244 13360 Vigna umbellata 87088 TAG|GTCAGTAATT...TTTGTTTTCACC/TTTGTTTTCACC...TTCAG|CAT 2 1 45.083
209727191 GT-AG 0 1.4078861360460908e-05 82 rna-XM_047306398.1 37986797 3 13436 13517 Vigna umbellata 87088 AGG|GTACGATGTT...GTTTTTGTGATT/GTTTTTGTGATT...TTCAG|AAA 2 1 51.61
209727192 GT-AG 0 0.0001431257638637 570 rna-XM_047306398.1 37986797 4 13660 14229 Vigna umbellata 87088 AAA|GTAATCCTCC...ACTGCCTGATTA/TGATTATTTATA...TGCAG|GTA 0 1 63.969
209727193 GT-AG 0 1.000000099473604e-05 84 rna-XM_047306398.1 37986797 5 14300 14383 Vigna umbellata 87088 TTG|GTGAGGAAAA...AAGTTTTTACAT/AAAGTTTTTACA...AACAG|GAT 1 1 70.061
209727194 GT-AG 0 0.0003745487516276 1301 rna-XM_047306398.1 37986797 6 14450 15750 Vigna umbellata 87088 GAG|GTATAACTCC...CAGTTTTTAGTG/TAGTGCCTAATA...AGCAG|CTG 1 1 75.805
209727195 GT-AG 0 1.000000099473604e-05 137 rna-XM_047306398.1 37986797 7 15874 16010 Vigna umbellata 87088 CAA|GTAAGTCCCT...TAACTCTTTCTT/TGATGGTTGATT...TGCAG|TTT 1 1 86.51

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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]);