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 = 28258297

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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
156963663 GT-AG 0 1.000000099473604e-05 85 rna-XM_027181998.1 28258297 1 455965 456049 Pocillopora damicornis 46731 ATG|GTGAGATTCT...GATATTTTAAAA/TTGGTTGTGATT...TACAG|CGT 2 1 2.167
156963664 GT-AG 0 1.000000099473604e-05 968 rna-XM_027181998.1 28258297 2 456191 457158 Pocillopora damicornis 46731 CAG|GTGAGTATGT...TCTCTCTTGTTA/ATTTTGTTCAAA...CACAG|CTT 2 1 13.917
156963665 GT-AG 0 1.000000099473604e-05 171 rna-XM_027181998.1 28258297 3 457271 457441 Pocillopora damicornis 46731 CAT|GTGAGTATTA...AACTTCTTCCCA/ACACTTTTCATA...ACTAG|TTG 0 1 23.25
156963666 GT-AG 0 1.000000099473604e-05 411 rna-XM_027181998.1 28258297 4 457529 457939 Pocillopora damicornis 46731 GAG|GTAAGTGCTG...TGATCCTAAATT/CATTTTTTCATT...TCAAG|CTT 0 1 30.5
156963667 GT-AG 0 0.000718308616043 535 rna-XM_027181998.1 28258297 5 458009 458543 Pocillopora damicornis 46731 GAG|GTATTGTTAT...TTTTTTTTTGTC/GAGTTGTTTAGA...TTCAG|ACT 0 1 36.25
156963668 GT-AG 0 1.000000099473604e-05 646 rna-XM_027181998.1 28258297 6 458757 459402 Pocillopora damicornis 46731 TTG|GTTAGTGATT...TCTATGTTAACC/TCTATGTTAACC...TCTAG|GCT 0 1 54.0
156963669 GT-AG 0 1.000000099473604e-05 589 rna-XM_027181998.1 28258297 7 459739 460327 Pocillopora damicornis 46731 CAG|GTTGTTATAT...TCAACCTTTGTT/GTTTGTGTCAAC...GTCAG|GGA 0 1 82.0

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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]);