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 = 29350732

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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
163479846 GT-AG 0 0.0086067887325318 491 rna-XM_034357019.1 29350732 1 1049134 1049624 Prunus dulcis 3755 CAG|GTATATTTCT...TTACTCTTGTTC/CTCTTGTTCACT...TGCAG|ATG 0 1 54.444
163479847 GT-AG 0 0.0133817463577937 104 rna-XM_034357019.1 29350732 2 1049758 1049861 Prunus dulcis 3755 AAA|GTACTCATCC...ATTTTTTTACTT/AATTTTTTTACT...TGTAG|GTC 1 1 57.728
163479848 GT-AG 0 0.0186849900183332 739 rna-XM_034357019.1 29350732 3 1049951 1050689 Prunus dulcis 3755 GAG|GTATTTATTT...CAAACTTTAATT/CAAACTTTAATT...TTTAG|CTC 0 1 59.926
163479849 GT-AG 0 1.000000099473604e-05 298 rna-XM_034357019.1 29350732 4 1050914 1051211 Prunus dulcis 3755 TGG|GTAAGCGCTG...TTTATTTTCTCT/TAATGATTTATT...ATTAG|ATC 2 1 65.457
163479850 GT-AG 0 0.0014664479680175 770 rna-XM_034357019.1 29350732 5 1051299 1052068 Prunus dulcis 3755 CAG|GTACATTCTC...GTTCTTTTAAAT/GTTCTTTTAAAT...GTTAG|GTT 2 1 67.605
163479851 GT-AG 0 1.000000099473604e-05 155 rna-XM_034357019.1 29350732 6 1052169 1052323 Prunus dulcis 3755 TCG|GTAAAGCTAT...GTTTTCTTATAT/TGTTTTCTTATA...TGAAG|GCT 0 1 70.074
163479852 GT-AG 0 1.000000099473604e-05 101 rna-XM_034357019.1 29350732 7 1052535 1052635 Prunus dulcis 3755 CAG|GTTCTATTTA...TTTTCCTTTCCA/CTCATTTTCACC...AATAG|ATT 1 1 75.284

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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]);