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 = 8933519

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id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
48130601 GT-AG 0 4.095666252709529e-05 104 rna-XM_027307970.1 8933519 1 34703697 34703800 Coffea eugenioides 49369 CAG|GTACTGTCTT...CCTTTTTTATCC/CTTGTACTTATT...TCCAG|GTC 2 1 27.28
48130602 GT-AG 0 0.00093399920228 3214 rna-XM_027307970.1 8933519 2 34704413 34707626 Coffea eugenioides 49369 GGT|GTAAGTTCCA...ATGTTTTTAACC/ATGTTTTTAACC...TTCAG|GTT 2 1 38.714
48130603 GT-AG 0 1.000000099473604e-05 985 rna-XM_027307970.1 8933519 3 34708750 34709734 Coffea eugenioides 49369 AAG|GTAATAAATT...TATATCTTAAAT/TATATCTTAAAT...GCCAG|TTA 0 1 59.697
48130604 GT-AG 0 1.000000099473604e-05 86 rna-XM_027307970.1 8933519 4 34710024 34710109 Coffea eugenioides 49369 AAG|GTAAATGGTC...TTTATCTTTTCA/TATCTTTTCAAT...TGCAG|CTG 1 1 65.097
48130605 GT-AG 0 0.0601516545132245 291 rna-XM_027307970.1 8933519 5 34710235 34710525 Coffea eugenioides 49369 CAA|GTATGTTTGG...AACTTTTTATCT/CAACTTTTTATC...TCCAG|GTC 0 1 67.433
48130606 GT-AG 0 0.0017393597011209 1493 rna-XM_027307970.1 8933519 6 34710984 34712476 Coffea eugenioides 49369 CAG|GTATTGTTAG...CATATCTTGATT/ATTGTATTAATC...TGCAG|GGA 2 1 75.99
48130607 GT-AG 0 0.0028102424515747 1096 rna-XM_027307970.1 8933519 7 34712506 34713601 Coffea eugenioides 49369 AAG|GTAACCACTC...CTTTTTTCAATC/GCTTTTTTCAAT...ATCAG|GTT 1 1 76.532
48130608 GT-AG 0 1.000000099473604e-05 435 rna-XM_027307970.1 8933519 8 34714196 34714630 Coffea eugenioides 49369 GAG|GTAAATAGAT...TATTTCTTATAA/CTATTTCTTATA...TGCAG|ATT 1 1 87.631

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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]);