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 = 35543725

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Suggested facets: score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
199805323 GT-AG 0 1.000000099473604e-05 6946 rna-gnl|WGS:VXBI|TOXRED_R04909_mrna 35543725 1 1199174 1206119 Toxostoma redivivum 99882 AAG|GTGAGCCCGG...ATTTCTTTATTT/CATTTCTTTATT...TACAG|AAA 1 1 10.562
199805324 GT-AG 0 1.000000099473604e-05 1038 rna-gnl|WGS:VXBI|TOXRED_R04909_mrna 35543725 2 1197994 1199031 Toxostoma redivivum 99882 AAG|GTAAAAGGGC...CTGGCCTGAAAA/TGTTATTTCAGC...CTCAG|GAA 2 1 20.302
199805325 GT-AG 0 1.000000099473604e-05 720 rna-gnl|WGS:VXBI|TOXRED_R04909_mrna 35543725 3 1197133 1197852 Toxostoma redivivum 99882 AAG|GTAAAATTTG...GAATGCTGAAAT/AAATAACTCATC...TGCAG|AAG 2 1 29.973
199805326 GT-AG 0 1.000000099473604e-05 1390 rna-gnl|WGS:VXBI|TOXRED_R04909_mrna 35543725 4 1195584 1196973 Toxostoma redivivum 99882 GAA|GTGAGTAGTG...GTGCCCTGAGGT/AGTGCCCTGAGG...GGCAG|GCA 2 1 40.878
199805327 GT-AG 0 4.485126425719151e-05 2478 rna-gnl|WGS:VXBI|TOXRED_R04909_mrna 35543725 5 1192931 1195408 Toxostoma redivivum 99882 CAG|GTATGGCTGG...TTGTACTTGACT/TTGTACTTGACT...TTTAG|GCA 0 1 52.881
199805328 GT-AG 0 1.000000099473604e-05 649 rna-gnl|WGS:VXBI|TOXRED_R04909_mrna 35543725 6 1192089 1192737 Toxostoma redivivum 99882 AAG|GTGGGACTAG...AAAGCCTTACTG/CAAAGCCTTACT...TCCAG|ATT 1 1 66.118
199805329 GT-AG 0 1.000000099473604e-05 852 rna-gnl|WGS:VXBI|TOXRED_R04909_mrna 35543725 7 1190952 1191803 Toxostoma redivivum 99882 AAG|GTAAGCATGC...CTTTTTTTCCCT/CCCATGTTCACT...TGCAG|AAA 1 1 85.665

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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]);