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 = 23617058

✎ 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
128510344 GT-AG 0 1.000000099473604e-05 138 rna-XM_019398322.1 23617058 1 4300112 4300249 Nicotiana attenuata 49451 AAG|GTGCTGCAAC...CTTTCTTTATTT/TCTTTCTTTATT...GTTAG|TGG 1 1 45.283
128510345 GT-AG 0 1.000000099473604e-05 560 rna-XM_019398322.1 23617058 2 4300557 4301116 Nicotiana attenuata 49451 AAG|GTAATATTAA...TTGCCTATAACA/GCTATGTTGATT...TGCAG|GTT 2 1 53.582
128510346 GT-AG 0 1.000000099473604e-05 145 rna-XM_019398322.1 23617058 3 4301811 4301955 Nicotiana attenuata 49451 CTG|GTAATGCTTG...TGCTCTTTGTTT/AAACTGTTCATT...TGCAG|CTA 0 1 72.344
128510347 GT-AG 0 1.000000099473604e-05 86 rna-XM_019398322.1 23617058 4 4302080 4302165 Nicotiana attenuata 49451 ATG|GTAAGTGTTA...CTGATCTAAAAT/GCAATACTGATC...TACAG|GTG 1 1 75.696
128510348 GT-AG 0 1.02489204413458e-05 391 rna-XM_019398322.1 23617058 5 4302386 4302776 Nicotiana attenuata 49451 CTG|GTAAGTGTAC...TTTTCTTTAAAT/TTTTCTTTAAAT...CTCAG|GTA 2 1 81.644
128510349 GT-AG 0 1.000000099473604e-05 143 rna-XM_019398322.1 23617058 6 4303236 4303378 Nicotiana attenuata 49451 CTG|GTAAGATCAC...TTGCTTGTAAAA/TAGAGACTGATT...TGCAG|GGC 2 1 94.052

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]);