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)

7 rows where transcript_id = 5879254

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Suggested facets: dinucleotide_pair, score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
29939520 GT-AG 0 1.000000099473604e-05 1056 rna-XM_014962774.1 5879254 1 120887 121942 Calidris pugnax 198806 CAG|GTGGGCAGGG...TTTTCCTTCCTG/CCGTTGCTGACC...TTCAG|GGT 2 1 5.011
29939521 GT-AG 0 1.000000099473604e-05 969 rna-XM_014962774.1 5879254 2 119780 120748 Calidris pugnax 198806 GAG|GTAGGGGGTG...TTCCTCTTCTCA/CCTCTTCTCACA...CCCAG|GCT 2 1 12.289
29939522 GC-AG 0 1.000000099473604e-05 258 rna-XM_014962774.1 5879254 3 118425 118682 Calidris pugnax 198806 CAG|GCCATAAGGA...TGGTTCTCAGAG/GTGGTTCTCAGA...CACAG|GCC 1 1 70.148
29939523 GT-AG 0 3.5060541450083126e-05 240 rna-XM_014962774.1 5879254 4 118108 118347 Calidris pugnax 198806 GAG|GTAGGGTTTT...CATTTTTTAATC/CATTTTTTAATC...CTCAG|ATT 0 1 74.209
29939524 GT-AG 0 1.000000099473604e-05 2011 rna-XM_014962774.1 5879254 5 115924 117934 Calidris pugnax 198806 CCA|GTGAGTACCT...GTTTTCTTTTCA/GTCGTATTAATG...TTTAG|CGA 2 1 83.333
29939525 GT-AG 0 0.0001611136926906 446 rna-XM_014962774.1 5879254 6 115407 115852 Calidris pugnax 198806 CAG|GTACCAGTGA...CAATCTTTGTTC/GGTCTGCTAATT...TGCAG|CAT 1 1 87.078
29939526 GT-AG 0 1.000000099473604e-05 1998 rna-XM_014962774.1 5879254 7 113313 115310 Calidris pugnax 198806 CAA|GTAAGACAAT...TGTTCCTCAACG/ATTTTTTTCACC...CCTAG|AAC 1 1 92.141

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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]);