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 = 9114909

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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
49389934 GT-AG 0 1.000000099473604e-05 966 rna-gnl|WGS:VYZG|COLPIC_R04159_mrna 9114909 1 2897407 2898372 Columbina picui 115618 AAG|GTAAGAAGCC...CACTTCTTTGTG/GGGTCACTGACT...TCCAG|GAC 0 1 10.408
49389935 GT-AG 0 1.000000099473604e-05 102 rna-gnl|WGS:VYZG|COLPIC_R04159_mrna 9114909 2 2898529 2898630 Columbina picui 115618 CTG|GTGAGTAACT...GTGCTGGTAACC/GTGCTGGTAACC...TTCAG|CGC 0 1 21.02
49389936 GT-AG 0 1.000000099473604e-05 668 rna-gnl|WGS:VYZG|COLPIC_R04159_mrna 9114909 3 2898717 2899384 Columbina picui 115618 AGT|GTCAGGCCTT...TTGGCCACAAAT/CCACAAATCATG...TACAG|TGC 2 1 26.871
49389937 GT-AG 0 1.000000099473604e-05 342 rna-gnl|WGS:VYZG|COLPIC_R04159_mrna 9114909 4 2899623 2899964 Columbina picui 115618 AAT|GTGAGCCAAT...TGAGCTTTGCAT/CTGGGTCCCACT...TGCAG|ATT 0 1 43.061
49389938 GT-AG 0 1.000000099473604e-05 371 rna-gnl|WGS:VYZG|COLPIC_R04159_mrna 9114909 5 2900081 2900451 Columbina picui 115618 AGG|GTCCAGGCAA...GGGGCTCCAGCT/TCCAGCTGCAGA...GCAAG|CAT 2 1 50.952
49389939 GT-AG 0 1.000000099473604e-05 243 rna-gnl|WGS:VYZG|COLPIC_R04159_mrna 9114909 6 2900729 2900971 Columbina picui 115618 CAG|GTGAGCTGAT...CTCTTCTGAATG/ACTCTTCTGAAT...GGCAG|GAC 0 1 69.796
49389940 GT-AG 0 1.000000099473604e-05 849 rna-gnl|WGS:VYZG|COLPIC_R04159_mrna 9114909 7 2901139 2901987 Columbina picui 115618 GAG|GTGAGTGCAG...TCCTTCTTAAAA/GAATTGTTGACA...TTGAG|TGT 2 1 81.156

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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]);