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 = 25340356

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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
139664513 GT-AG 0 2.0052302109600856e-05 600 rna-XM_007940871.1 25340356 1 26139017 26139616 Orycteropus afer 9818 CCG|GTACGTAAAG...TCTTCCTTTCCC/CTCTCCTCCACC...TGCAG|CTC 1 1 0.298
139664514 GT-AG 0 1.000000099473604e-05 459 rna-XM_007940871.1 25340356 2 26139772 26140230 Orycteropus afer 9818 CAG|GTGAGGAGCG...CCTCTCTGAACC/CCCTCTCTGAAC...GGTAG|GAC 0 1 6.888
139664515 GT-AG 0 5.566202207658386e-05 8006 rna-XM_007940871.1 25340356 3 26140354 26148359 Orycteropus afer 9818 GCG|GTAAGTCTCG...TGTCCCATAACA/ATATGTCCCATA...TCCAG|ACA 0 1 12.117
139664516 GT-AG 0 0.0003197466384658 44126 rna-XM_007940871.1 25340356 4 26149720 26193845 Orycteropus afer 9818 CAG|GTATGTCTAT...TGCTTCTCATCT/CTGCTTCTCATC...TTTAG|ATA 1 1 69.94
139664517 GT-AG 0 0.000284230666062 6190 rna-XM_007940871.1 25340356 5 26194039 26200228 Orycteropus afer 9818 GAG|GTATGCACAT...AATATTTTCATG/AATATTTTCATG...TTCAG|AGG 2 1 78.146
139664518 GT-AG 0 1.000000099473604e-05 3282 rna-XM_007940871.1 25340356 6 26200426 26203707 Orycteropus afer 9818 CAG|GTTACTGATA...GAATTTTTAAAA/AAATAACTTATT...AACAG|GTG 1 1 86.522

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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]);