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 = 20937013

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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
112209492 GT-AG 0 1.000000099473604e-05 43632 rna-XM_027949793.1 20937013 1 29273523 29317154 Marmota flaviventris 93162 ATG|GTAAGTGTCC...TAAATTTTATCT/AGTTTATTTATT...TTTAG|GAA 1 1 3.062
112209493 GT-AG 0 1.000000099473604e-05 21043 rna-XM_027949793.1 20937013 2 29252423 29273465 Marmota flaviventris 93162 CTG|GTAAGTCATT...GTGTTCTAAAGT/TGTGTTCTAAAG...TCCAG|CTT 1 1 5.271
112209494 GT-AG 0 1.000000099473604e-05 6759 rna-XM_027949793.1 20937013 3 29245528 29252286 Marmota flaviventris 93162 AAG|GTAATTCTGA...CTTTTCTGACCT/ACTTTTCTGACC...TGTAG|TTT 2 1 10.543
112209495 GT-AG 0 5.02386198679396e-05 1418 rna-XM_027949793.1 20937013 4 29243907 29245324 Marmota flaviventris 93162 CAG|GTGTGTTTTT...TTTTTCTTTCCC/CCCCTATTCATT...ACCAG|GAA 1 1 18.411
112209496 GT-AG 0 1.000000099473604e-05 1477 rna-XM_027949793.1 20937013 5 29241325 29242801 Marmota flaviventris 93162 AAG|GTCAGTATCA...TCTGCTTTGACC/ACACTTTTTATC...CAAAG|ATC 2 1 61.24
112209497 GT-AG 0 0.0157912422242286 4068 rna-XM_027949793.1 20937013 6 29237124 29241191 Marmota flaviventris 93162 CAG|GTATATTGTA...TCTTTCTTATTT/ATCTTTCTTATT...TGTAG|GCT 0 1 66.395

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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]);