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)

5 rows where transcript_id = 3395356

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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
16698975 GT-AG 0 0.0013219031105986 443 rna-gnl|WGS:VXAK|AREINT_R12500_mrna 3395356 1 4226 4668 Arenaria interpres 54971 GAG|GTAGGTTTCT...CTACTCTTAACT/CTACTCTTAACT...CCTAG|ATA 2 1 14.256
16698976 GT-AG 0 1.783249185697266 762 rna-gnl|WGS:VXAK|AREINT_R12500_mrna 3395356 2 4784 5545 Arenaria interpres 54971 GAG|GTATCCAGTA...TCTATTTTAAAA/AGTTTGTTTATC...CACAG|GTA 0 1 38.365
16698977 GT-AG 0 1.000000099473604e-05 152 rna-gnl|WGS:VXAK|AREINT_R12500_mrna 3395356 3 5634 5785 Arenaria interpres 54971 CTG|GTAAGTCCCA...AATCTCTTCTCT/CAGTAGTTAAAC...TCCAG|GTA 1 1 56.813
16698978 GT-AG 0 1.000000099473604e-05 87 rna-gnl|WGS:VXAK|AREINT_R12500_mrna 3395356 4 5848 5934 Arenaria interpres 54971 AAG|GTAGTGTAAT...TGTCTTTTGTCT/TCTTCGTTCACA...ACAAG|GTG 0 1 69.811
16698979 GT-AG 0 1.000000099473604e-05 350 rna-gnl|WGS:VXAK|AREINT_R12500_mrna 3395356 5 6059 6408 Arenaria interpres 54971 TAG|GTAAGGCTAA...TCAGACTTAAAT/ATATAACTTACG...TGCAG|GTG 1 1 95.807

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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]);