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 = 3555652

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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
17675667 GT-AG 0 1.000000099473604e-05 203 rna-XM_038316782.1 3555652 1 181153591 181153793 Arvicola amphibius 1047088 TCG|GTGTGTGCGG...TGTGTTTTGTCT/GCACCTCTCACA...CCAAG|GTC 2 1 1.45
17675668 GT-AG 0 1.000000099473604e-05 45088 rna-XM_038316782.1 3555652 2 181153868 181198955 Arvicola amphibius 1047088 AAA|GTAAGTGGCC...TTTATTTTATCC/TTTTATTTTATT...TTCAG|GAT 1 1 2.844
17675669 GT-AG 0 0.0001218488685952 518 rna-XM_038316782.1 3555652 3 181199022 181199539 Arvicola amphibius 1047088 AAG|GTATTAAAAA...TTTTCCTTACTT/GTTTTCCTTACT...TGCAG|AGT 1 1 4.087
17675670 GT-AG 0 0.0027362890807106 16995 rna-XM_038316782.1 3555652 4 181199620 181216614 Arvicola amphibius 1047088 AAG|GTAACCAAGA...GAATTTTTAAAT/GAATTTTTAAAT...TGCAG|GGA 0 1 5.593
17675671 GT-AG 0 2.579182636546725e-05 6158 rna-XM_038316782.1 3555652 5 181216748 181222905 Arvicola amphibius 1047088 AAG|GTTGGTTTTG...TTTACCTTAATG/TTTTTTTTTACC...TACAG|ACA 1 1 8.098
17675672 GT-AG 0 0.0030212158036064 3034 rna-XM_038316782.1 3555652 6 181223194 181226227 Arvicola amphibius 1047088 AAG|GTATGGTTTG...CAGCTCTTAATG/ATTTGCTTCAGC...TACAG|ACG 1 1 13.522
17675673 GT-AG 0 1.000000099473604e-05 26131 rna-XM_038316782.1 3555652 7 181226322 181252452 Arvicola amphibius 1047088 CGG|GTAAGGAAAA...TTTTTCTTTGTT/CACTTACTAATT...TCTAG|TGA 2 1 15.292

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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]);