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)

6 rows where transcript_id = 864962

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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
4311503 GT-AG 0 1.000000099473604e-05 1349 rna-gnl|WGS:WEIU|AEGCAU_R12859_mrna 864962 1 23802 25150 Aegithalos caudatus 73327 AAG|GTAAGAGTGG...ACAATTTTCCTT/TTAAATACAATT...TAAAG|CCT 2 1 4.881
4311504 GT-AG 0 6.871081117897781e-05 506 rna-gnl|WGS:WEIU|AEGCAU_R12859_mrna 864962 2 25209 25714 Aegithalos caudatus 73327 CAG|GTATGTCATT...CTGCCATTATTT/CCATTATTTATA...AACAG|GTT 0 1 10.903
4311505 GT-AG 0 1.000000099473604e-05 700 rna-gnl|WGS:WEIU|AEGCAU_R12859_mrna 864962 3 25793 26492 Aegithalos caudatus 73327 CAG|GTGAGTGGTA...AATATTTTCACA/AATATTTTCACA...CACAG|GGT 0 1 19.003
4311506 GT-AG 0 1.2240541446612436e-05 2313 rna-gnl|WGS:WEIU|AEGCAU_R12859_mrna 864962 4 26594 28906 Aegithalos caudatus 73327 AAG|GTATTGCAAT...AAATCCTTCTCT/TGATTTTTCATA...TTTAG|AGA 2 1 29.491
4311507 GT-AG 0 1.000000099473604e-05 429 rna-gnl|WGS:WEIU|AEGCAU_R12859_mrna 864962 5 28964 29392 Aegithalos caudatus 73327 AGG|GTAAGTATAG...ACGTTGTTAATT/TTAATTCTTACG...TACAG|GTT 2 1 35.41
4311508 GT-AG 0 0.0012238767638804 1835 rna-gnl|WGS:WEIU|AEGCAU_R12859_mrna 864962 6 29451 31285 Aegithalos caudatus 73327 CAG|GTAACTTACA...ATGATTTTGAAG/ATGATTTTGAAG...TGTAG|AGT 0 1 41.433

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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]);