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 = 1341785

✎ View and edit SQL

This data as json, CSV (advanced)

Suggested facets: phase, in_cds

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
7217767 GT-AG 0 0.0007065092721537 1643 rna-XM_020676482.1 1341785 2 2384403 2386045 Amborella trichopoda 13333 TCC|GTAAGTACCA...TTTTCTTTGATG/TTTTCTTTGATG...CTCAG|ATT 1 1 29.034
7217768 GT-AG 0 0.018989486002202 1655 rna-XM_020676482.1 1341785 3 2386090 2387744 Amborella trichopoda 13333 CTG|GTATGTGTTG...TTTTCTTTAACG/TTTTCTTTTATT...CACAG|ACC 0 1 31.369
7217769 GT-AG 0 0.1137746299820915 704 rna-XM_020676482.1 1341785 4 2387901 2388604 Amborella trichopoda 13333 TTG|GTACGCTCTC...CTTTCCTTAATA/TCTTTCCTTAAT...TTTAG|CTG 0 1 39.65
7217770 GT-AG 0 1.000000099473604e-05 836 rna-XM_020676482.1 1341785 5 2389160 2389995 Amborella trichopoda 13333 GAG|GTGAGCATTG...TAATTGTTGATG/TAATTGTTGATG...TTCAG|CTT 0 1 69.108
7217771 GT-AG 0 3.646603421169294e-05 304 rna-XM_020676482.1 1341785 6 2390299 2390602 Amborella trichopoda 13333 CTG|GTAAGCCTTC...TTAATCTTCATT/TTAATCTTCATT...TGTAG|AAT 0 1 85.191
7218071 GT-AG 0 0.0001997750364619 1687 rna-XM_020676482.1 1341785 1 2382444 2384130 Amborella trichopoda 13333 AAG|GTAAATTGTG...TTCTTCTTGACT/CATGTATTTACT...AACAG|GCT   0 18.153

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]);