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 = 8855956

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Suggested facets: score, 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
47813756 GT-AG 0 1.000000099473604e-05 518 rna-XM_027244017.1 8855956 2 19674796 19675313 Coffea arabica 13443 AGT|GTGAGTCAAA...TTTTCCTGAATA/ATTTTCCTGAAT...TTTAG|GCT 0 1 15.343
47813757 GT-AG 0 1.000000099473604e-05 76 rna-XM_027244017.1 8855956 3 19673974 19674049 Coffea arabica 13443 AAG|GTACTAGATT...TAATTTTTAATG/ATCATACTAATT...CTCAG|GTT 2 1 39.238
47813758 GT-AG 0 3.328319952744246e-05 88 rna-XM_027244017.1 8855956 4 19673414 19673501 Coffea arabica 13443 AAG|GTATAGACTA...TTTCCTTTCATT/TTTCCTTTCATT...TGCAG|GTA 0 1 54.356
47813759 GT-AG 0 1.000000099473604e-05 1254 rna-XM_027244017.1 8855956 5 19671992 19673245 Coffea arabica 13443 ACG|GTGAGTTACT...GTGTTTTTGAAT/GTGTTTTTGAAT...GACAG|GTT 0 1 59.737
47813760 GT-AG 0 0.0001424703314153 1344 rna-XM_027244017.1 8855956 6 19670393 19671736 Coffea arabica 13443 AAG|GTATGGTCCA...TTGGTTTTAGTT/CCGTATTTTATT...TGCAG|GTC 0 1 67.905
47813761 GT-AG 0 1.000000099473604e-05 138 rna-XM_027244017.1 8855956 7 19670132 19670269 Coffea arabica 13443 GAG|GTGAGATTAT...TTATCTTAGAAA/AATTTAGTCACA...TGCAG|TCC 0 1 71.845
47813762 GT-AG 0 2.984000762066345e-05 991 rna-XM_027244017.1 8855956 8 19668655 19669645 Coffea arabica 13443 CAG|GTAGGTTCTC...ATTTTATTAACA/ATTTTATTAACA...TACAG|TTG 0 1 87.412
47819620 GT-AG 0 1.000000099473604e-05 507 rna-XM_027244017.1 8855956 1 19675606 19676112 Coffea arabica 13443 TTG|GTTAGTTTTC...GACAATTTGATT/ATTTGATTGATA...GTCAG|ATT   0 6.598

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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]);