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 = 30001180

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Suggested facets: dinucleotide_pair, score, length, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
168077767 TA-TC 0 0.0213211136459784 742 rna-XM_018651155.1 30001180 1 1715971 1716712 Pyrus x bretschneideri 225117 CGG|TATTTATCTC...GGGTTCTTCACT/GGGTTCTTCACT...GGTTC|GGT 2 1 7.98
168077768 GT-AG 0 1.000000099473604e-05 99 rna-XM_018651155.1 30001180 2 1714739 1714837 Pyrus x bretschneideri 225117 TAG|GTAAACAAAC...CAATTCATAAAT/ACGTTACTCATT...TTCAG|ATG 1 1 52.516
168077769 GT-AG 0 1.000000099473604e-05 144 rna-XM_018651155.1 30001180 3 1714487 1714630 Pyrus x bretschneideri 225117 CCG|GTAAGAGAAT...ATAACCTTGTTG/CCATTACTCAAT...AATAG|GGA 1 1 56.761
168077770 GT-AG 0 1.000000099473604e-05 122 rna-XM_018651155.1 30001180 4 1714168 1714289 Pyrus x bretschneideri 225117 AAG|GTGACTGTAT...GCATGTTTAATT/GTTTAATTTATA...TGTAG|GGT 0 1 64.505
168077771 GT-AG 0 1.000000099473604e-05 160 rna-XM_018651155.1 30001180 5 1713797 1713956 Pyrus x bretschneideri 225117 TTG|GTTAGTTTCA...TATTGCTTACAT/TTATTGCTTACA...ATTAG|ATC 1 1 72.799
168077772 GT-AG 0 1.000000099473604e-05 99 rna-XM_018651155.1 30001180 6 1713460 1713558 Pyrus x bretschneideri 225117 ACG|GTAAGGGTCA...CAGTTATTAATA/CAGTTATTAATA...TGCAG|TGG 2 1 82.154
168077773 GT-AG 0 4.055534570882526e-05 105 rna-XM_018651155.1 30001180 7 1713204 1713308 Pyrus x bretschneideri 225117 CAT|GTAAGCTAAT...CAGATTCTAACA/CAGATTCTAACA...GTCAG|GTT 0 1 88.09

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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]);