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 = 9992687

✎ 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
54887707 GT-AG 0 1.000000099473604e-05 86 rna-XM_009558971.1 9992687 1 4461 4546 Cuculus canorus 55661 GAG|GTACGAAGGG...TGTTCTTTGCCT/CGGGTGTTGAAG...CGCAG|CAC 0 1 12.76
54887708 GT-AG 0 0.0001152614015137 92 rna-XM_009558971.1 9992687 2 4700 4791 Cuculus canorus 55661 GAG|GTAAACGCCG...CTTTCTTTGATG/CTTTCTTTGATG...CGCAG|AGC 0 1 27.893
54887709 GT-AG 0 1.000000099473604e-05 1169 rna-XM_009558971.1 9992687 3 4855 6023 Cuculus canorus 55661 ATG|GTGAGTGTCC...GGTCCCCTAACC/GGTCCCCTAACC...CCCAG|AAG 0 1 34.125
54887710 GT-AG 0 7.982238283700397e-05 134 rna-XM_009558971.1 9992687 5 7925 8058 Cuculus canorus 55661 TGG|GTATAGGAAG...GTTTTTTTAATG/GTTTTTTTAATG...CCCAG|TGT 1 1 48.467
54887711 GT-AG 0 1.119047383417851e-05 87 rna-XM_009558971.1 9992687 7 8400 8486 Cuculus canorus 55661 TCG|GTGCGTTCAG...CCCGTTTTAACG/CCCGTTTTAACG...CCCAG|ACC 1 1 73.393
54887712 GT-AG 0 1.000000099473604e-05 81 rna-XM_009558971.1 9992687 8 8615 8695 Cuculus canorus 55661 AAG|GTGGGCCTGG...ATCCCCTCACCC/GATCCCCTCACC...CGAAG|GTG 0 1 86.053

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]);