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)

8 rows where transcript_id = 25340418

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Suggested facets: score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
139665093 GT-AG 0 1.000000099473604e-05 585 rna-XM_007949832.1 25340418 1 4790894 4791478 Orycteropus afer 9818 CCG|GTACGTGGAA...AGATTCTGGGCA/CTGTGAATAATA...TTAAG|ATG 1 1 1.184
139665094 GT-AG 0 1.000000099473604e-05 1876 rna-XM_007949832.1 25340418 2 4791619 4793494 Orycteropus afer 9818 CAG|GTAATGGACT...TTGTTCTCATTT/TTTGTTCTCATT...TATAG|GTG 0 1 13.934
139665095 GT-AG 0 1.000000099473604e-05 150 rna-XM_007949832.1 25340418 3 4793727 4793876 Orycteropus afer 9818 ACA|GTGAGTCTGT...TGTTTCTTCTAT/TCTATGTGTATA...CACAG|TCA 1 1 35.064
139665096 GT-AG 0 0.000350165078111 1338 rna-XM_007949832.1 25340418 4 4793950 4795287 Orycteropus afer 9818 TCA|GTAAGTATTA...TAACTTTTATCT/ATAACTTTTATC...CACAG|AAG 2 1 41.712
139665097 GT-AG 0 2.2075779337397094e-05 1058 rna-XM_007949832.1 25340418 5 4795382 4796439 Orycteropus afer 9818 AAG|GTAGGCATCT...TTATTTTTTTCC/GTGTCATTTATT...CACAG|TAT 0 1 50.273
139665098 GT-AG 0 1.000000099473604e-05 74 rna-XM_007949832.1 25340418 6 4796555 4796628 Orycteropus afer 9818 TAG|GTAGGTGAAT...TCTATTTTGGTA/ATTTTGGTAAAG...TATAG|CTT 1 1 60.747
139665099 GT-AG 0 1.000000099473604e-05 4171 rna-XM_007949832.1 25340418 8 4798442 4802612 Orycteropus afer 9818 CTG|GTGTGCATCT...TCAAATATGACC/TCAAATATGACC...TTTAG|GAA 2 1 71.767
139665100 GT-AG 0 3.5981088509822e-05 891 rna-XM_007949832.1 25340418 9 4802790 4803680 Orycteropus afer 9818 AAA|GTAAGCGAGC...GATTTTTTAAAA/GATTTTTTAAAA...ATTAG|ATT 2 1 87.887

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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]);