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)

6 rows where transcript_id = 12947857

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Suggested facets: phase, in_cds

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
69094793 GT-AG 0 0.0060029554529172 2282 rna-XM_010939987.3 12947857 4 42432537 42434818 Elaeis guineensis 51953 CAG|GTATGCACTT...GCATCTTTATAT/TATATTTTCACT...GACAG|ACA 1 1 12.911
69094794 GT-AG 0 4.796579453954045e-05 252 rna-XM_010939987.3 12947857 5 42430507 42430758 Elaeis guineensis 51953 CAG|GTAGATGTTT...TTTTTTTTAATG/TTTTTTTTAATG...ATCAG|GTG 0 1 44.661
69094795 GT-AG 0 1.048802451639653e-05 486 rna-XM_010939987.3 12947857 6 42428041 42428526 Elaeis guineensis 51953 AAG|GTAATTTTTA...TGATTTCTAAAG/TGATTTCTAAAG...TCCAG|GAA 0 1 80.018
69105258 GT-AG 0 0.0001599223244255 511 rna-XM_010939987.3 12947857 1 42435444 42435954 Elaeis guineensis 51953 ACG|GTATGGTCTT...GGTTTTTGAATG/TGGTTACTGAAA...TGAAG|GTG   0 8.732
69105259 GT-AG 0 1.000000099473604e-05 111 rna-XM_010939987.3 12947857 2 42435274 42435384 Elaeis guineensis 51953 GAG|GTGGGGAAAA...GTTTTCTTATGT/TGTTTTCTTATG...ATCAG|GTG   0 9.786
69105260 GT-AG 0 0.0091785143849256 78 rna-XM_010939987.3 12947857 3 42435124 42435201 Elaeis guineensis 51953 GAG|GTATTCCTTA...CAAACCTGATCC/CCAAACCTGATC...TATAG|GTG   0 11.071

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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]);