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 = 12720341

✎ View and edit SQL

This data as json, CSV (advanced)

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
67623277 GT-AG 0 1.000000099473604e-05 412 rna-XM_009903894.1 12720341 1 880965 881376 Dryobates pubescens 118200 CAG|GTGCACATCA...GCGGGCTTGGCG/TGGCGTGTGACT...AGCAG|GGC 1 1 3.683
67623278 GT-AG 0 0.4702243164342461 4254 rna-XM_009903894.1 12720341 2 876663 880916 Dryobates pubescens 118200 CGG|GTCTCCTCCC...CTCTCTGTGACT/CTCTCTGTGACT...TGCAG|GGC 1 1 8.103
67623279 GT-AG 0 1.000000099473604e-05 992 rna-XM_009903894.1 12720341 3 875373 876364 Dryobates pubescens 118200 CCG|GTAGGTAGCT...TCTTCCTTGCCA/AGGGGCCTCAAG...CTTAG|GAA 2 1 35.543
67623280 GT-AG 0 1.000000099473604e-05 1348 rna-XM_009903894.1 12720341 4 873867 875214 Dryobates pubescens 118200 TAG|GTAAGGAATT...AACTCTTTCATC/TTTCATCTCACA...TCCAG|ATG 1 1 50.092
67623281 GT-AG 0 1.000000099473604e-05 839 rna-XM_009903894.1 12720341 5 872944 873782 Dryobates pubescens 118200 AAG|GTAAGTTGTG...CTCACTTTTACC/TGGAATCTCACT...CTTAG|GAC 1 1 57.827
67623282 GT-AG 0 1.000000099473604e-05 593 rna-XM_009903894.1 12720341 6 872248 872840 Dryobates pubescens 118200 GAG|GTAAGGGACA...TTCTCTTTGCCT/CCTCTCTTCACA...AGGAG|ACA 2 1 67.311

Advanced export

JSON shape: default, array, newline-delimited, object

CSV options: 

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]);