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 = 34283788

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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
192054435 GT-AG 0 1.000000099473604e-05 692 rna-XM_014877659.1 34283788 2 7274196 7274887 Sturnus vulgaris 9172 ATG|GTAAGAAGCC...GTTTTCTTCCAA/GTACTATTGAAA...TTCAG|CTT 1 1 41.457
192054436 GT-AG 0 1.000000099473604e-05 461 rna-XM_014877659.1 34283788 3 7273384 7273844 Sturnus vulgaris 9172 AGG|GTGCGTGTGC...AGTTTCCTATTG/TTGGCAATGATT...TTTAG|CTC 1 1 64.702
192054437 GT-AG 0 0.0043598811975829 839 rna-XM_014877659.1 34283788 4 7272263 7273101 Sturnus vulgaris 9172 CAG|GTAACATTTC...AACATCTTAATC/AACATCTTAATC...TGAAG|ATT 1 1 83.377
192054438 GT-AG 0 0.0003205438410115 1416 rna-XM_014877659.1 34283788 5 7270736 7272151 Sturnus vulgaris 9172 AAG|GTATGCAAAT...TTTTTTCTATTG/TTTTTTTCTATT...TTCAG|CTA 1 1 90.728
192054439 GT-AG 0 0.0012248966743734 909 rna-XM_014877659.1 34283788 6 7269776 7270684 Sturnus vulgaris 9172 CAA|GTATGTACAT...ATGTCCTTTGCT/GCTATGCTCACG...TACAG|AGC 1 1 94.106
192054440 GT-AG 0 1.6456016615097874e-05 946 rna-XM_014877659.1 34283788 7 7268764 7269709 Sturnus vulgaris 9172 AAT|GTAAGTATAA...CATTCTGTAATT/CATTTTTTCACA...TACAG|ATA 1 1 98.477
192054556 GT-AG 0 4.194388331794066e-05 2148 rna-XM_014877659.1 34283788 1 7274957 7277104 Sturnus vulgaris 9172 TTT|GTAAGTAGTA...GTATTTTTATTT/TGTATTTTTATT...TTTAG|GTT   0 37.815

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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]);