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 = 15198718

✎ 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
82238009 GT-AG 0 0.0013098434450252 2156 rna-XM_005415623.2 15198718 1 8840990 8843145 Geospiza fortis 48883 GGG|GTACTCAGGT...ATATTGTTAATA/ATATTGTTAATA...CACAG|ATA 1 1 3.11
82238010 GT-AG 0 1.000000099473604e-05 4953 rna-XM_005415623.2 15198718 2 8843235 8848187 Geospiza fortis 48883 CAG|GTAGGTTTCG...TGTTGCATACTA/TGATAAGTAACT...TCCAG|GTC 0 1 4.808
82238011 GT-AG 0 1.000000099473604e-05 15774 rna-XM_005415623.2 15198718 3 8848305 8864078 Geospiza fortis 48883 GTT|GTGGGTATAA...TTTTCTGTAACT/AAAAATTTAATC...CATAG|GGC 0 1 7.041
82238012 GT-AG 0 1.5012015963507215e-05 1606 rna-XM_005415623.2 15198718 4 8864283 8865888 Geospiza fortis 48883 ACG|GTAAGTCACA...TGTTTTTTAACA/TGTTTTTTAACA...AAAAG|ATG 0 1 10.933
82238013 GT-AG 0 1.000000099473604e-05 301 rna-XM_005415623.2 15198718 5 8866034 8866334 Geospiza fortis 48883 CTG|GTAAAGTTCA...GTTCTCTTTTCA/TCTCTTTTCATC...CCCAG|CTA 1 1 13.7
82238014 GT-AG 0 1.000000099473604e-05 1481 rna-XM_005415623.2 15198718 6 8866925 8868405 Geospiza fortis 48883 AAG|GTAAATAAGT...TGTGCTTCATTG/CTGTGCTTCATT...TCTAG|GCC 0 1 24.957

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]);