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)

9 rows where transcript_id = 10113165

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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
55534793 GT-AG 0 0.0034948287591845 449 rna-XM_023083262.1 10113165 1 9273303 9273751 Cucurbita moschata 3662 CAG|GTACACGTTT...TGCTCTTTAATT/CTTTAATTCATC...CACAG|GTA 0 1 2.103
55534794 GT-AG 0 0.0001876443337084 98 rna-XM_023083262.1 10113165 2 9273950 9274047 Cucurbita moschata 3662 ATG|GTATTGCCTG...TATTCTGTAATT/TTTAAATTGAAT...CACAG|GGA 0 1 7.243
55534795 GT-AG 0 7.998567663220865e-05 148 rna-XM_023083262.1 10113165 3 9274171 9274318 Cucurbita moschata 3662 CAA|GTAAGCTCCA...TATTCCACAATT/TAATATCTGAAG...TGCAG|GTA 0 1 10.436
55534796 GT-AG 0 1.5027832161058268e-05 83 rna-XM_023083262.1 10113165 4 9274360 9274442 Cucurbita moschata 3662 GAG|GTCTGTATGA...TAGCCTTTAAGA/TACTGGATTATA...TTCAG|GAG 2 1 11.501
55534797 GT-AG 0 1.000000099473604e-05 452 rna-XM_023083262.1 10113165 5 9274612 9275063 Cucurbita moschata 3662 AAG|GTAAGATCGT...ATTTTTGTATCT/TTATAACTAACA...TGTAG|GAA 0 1 15.888
55534798 GT-AG 0 4.242898875005479e-05 84 rna-XM_023083262.1 10113165 6 9275230 9275313 Cucurbita moschata 3662 CAG|GTAATCATTC...TCATCTTTCATG/TAATGTCTCATC...GGAAG|CAG 1 1 20.197
55534799 GT-AG 0 1.000000099473604e-05 90 rna-XM_023083262.1 10113165 7 9277902 9277991 Cucurbita moschata 3662 ATA|GTCAGTCTCT...AACTGCTTAAAA/TGAGTGCTAATT...AACAG|AAT 0 1 87.383
55534800 GT-AG 0 1.000000099473604e-05 82 rna-XM_023083262.1 10113165 8 9278124 9278205 Cucurbita moschata 3662 AAG|GTAGAAAATG...AATTTCTTGTCC/AACTTGTTAATT...TATAG|GAT 0 1 90.81
55534801 GT-AG 0 1.000000099473604e-05 302 rna-XM_023083262.1 10113165 9 9278322 9278623 Cucurbita moschata 3662 CAG|GTAGGTTCAT...TTTCCCATATCT/CTCAATCTGAAT...TTCAG|GCT 2 1 93.821

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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]);