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 = 9114898

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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
49389842 GT-AG 0 1.000000099473604e-05 298 rna-gnl|WGS:VYZG|COLPIC_R04098_mrna 9114898 3 4533372 4533669 Columbina picui 115618 GGC|GTGCAGCAGC...CACCTGTGGGCG/TGGGCGCTGCGC...TGGAG|CCT 2 1 19.77
49389843 GT-AG 0 1.000000099473604e-05 76 rna-gnl|WGS:VYZG|COLPIC_R04098_mrna 9114898 4 4533761 4533836 Columbina picui 115618 CAG|GTAAGGCGCA...GAGCCCTGGACT/CCTGGACTGACC...CTCAG|GGC 0 1 25.0
49389844 GT-AG 0 1.000000099473604e-05 103 rna-gnl|WGS:VYZG|COLPIC_R04098_mrna 9114898 5 4534062 4534164 Columbina picui 115618 AAG|GTGAGCCTCG...CTCACTTTAACC/CTCACTTTAACC...CCTAG|ATC 0 1 37.931
49389845 GT-AG 0 1.000000099473604e-05 1574 rna-gnl|WGS:VYZG|COLPIC_R04098_mrna 9114898 6 4534441 4536014 Columbina picui 115618 AAG|GTACTGCCCC...CTCTCCTGAACT/CAGTTCCTAAGG...CACAG|GGA 0 1 53.793
49389846 GT-AG 0 1.000000099473604e-05 3319 rna-gnl|WGS:VYZG|COLPIC_R04098_mrna 9114898 7 4536171 4539489 Columbina picui 115618 AAG|GTAAGAAGCC...CTTCCTTTCTCT/ATGGCATTCAAA...CCCAG|GAG 0 1 62.759
49389847 GT-AG 0 1.000000099473604e-05 219 rna-gnl|WGS:VYZG|COLPIC_R04098_mrna 9114898 8 4539632 4539850 Columbina picui 115618 AGT|GTGAGCGCTG...AGTTCCTGCACT/CCTGCACTGACC...GTCAG|GCC 1 1 70.92
49389848 GT-AG 0 1.000000099473604e-05 291 rna-gnl|WGS:VYZG|COLPIC_R04098_mrna 9114898 9 4539997 4540287 Columbina picui 115618 GAT|GTAAGTGCCT...CCTCTCTTCCCC/AGGTATGTAACA...TCCAG|GGT 0 1 79.31

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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]);