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)

8 rows where transcript_id = 27592285

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Suggested facets: length, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
153481141 GT-AG 0 0.0003221737170403 210 rna-XM_024526035.1 27592285 1 11361283 11361492 Physcomitrium patens 3218 GCG|GTATGTGATT...TGTCTCCTGACA/TGTCTCCTGACA...AATAG|TTA 1 1 4.097
153481142 GT-AG 0 0.000309226061145 118 rna-XM_024526035.1 27592285 2 11361007 11361124 Physcomitrium patens 3218 CAT|GTCTGTTCGC...ATGTTTGTGATA/ATGTTTGTGATA...TGCAG|TTA 0 1 8.472
153481143 GT-AG 0 0.0008427786612506 246 rna-XM_024526035.1 27592285 3 11360626 11360871 Physcomitrium patens 3218 CAG|GTATGTTGCA...CATGTCATAATG/CAGCCACTCACA...TCCAG|AAG 0 1 12.209
153481144 GT-AG 0 2.0071811655858092e-05 249 rna-XM_024526035.1 27592285 4 11358806 11359054 Physcomitrium patens 3218 CAG|GTGTGTCTGA...CTTTTTTTGACC/CTTTTTTTGACC...GATAG|GTC 2 1 55.703
153481145 GT-AG 0 3.564574882452844e-05 246 rna-XM_024526035.1 27592285 5 11358482 11358727 Physcomitrium patens 3218 CAG|GTATGTGTAG...CCAAACTTACCG/TCCAAACTTACC...GATAG|ATC 2 1 57.863
153481146 GT-AG 0 0.0745968686636574 146 rna-XM_024526035.1 27592285 6 11357731 11357876 Physcomitrium patens 3218 CAG|GTATCGAATC...GAGGCCTTGACC/TGTTACTTGACT...AACAG|CTG 1 1 74.612
153481147 GT-AG 0 1.000000099473604e-05 162 rna-XM_024526035.1 27592285 7 11357285 11357446 Physcomitrium patens 3218 CAG|GTGCATCGAT...TGGTTCTAAGTA/ACAATGTTCATT...GCTAG|GTA 0 1 82.475
153481148 GT-AG 0 5.385465973585817e-05 105 rna-XM_024526035.1 27592285 8 11357039 11357143 Physcomitrium patens 3218 GAG|GTCTGTCTGT...AACTTCTTCACT/AACTTCTTCACT...CACAG|AGC 0 1 86.379

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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]);