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)

8 rows where transcript_id = 28932359

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Suggested facets: score, length, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
161300704 GT-AG 0 0.1250018149760131 106 rna-XM_024593900.1 28932359 1 26411497 26411602 Populus trichocarpa 3694 GAG|GTATTCCTTT...CTATTTTTAATT/CTATTTTTAATT...TTTAG|GAG 2 1 32.86
161300705 GT-AG 0 0.0015756407943206 431 rna-XM_024593900.1 28932359 2 26412218 26412648 Populus trichocarpa 3694 GGT|GTAAGTTTTT...CTTGCTTTAGTA/ATTTTTTTCATG...TGCAG|GTC 2 1 44.056
161300706 GT-AG 0 1.7353985429360953e-05 558 rna-XM_024593900.1 28932359 3 26413754 26414311 Populus trichocarpa 3694 AAA|GTAAGGATCC...TATCCCTTGATC/TTTAAATTCATC...TGCAG|TTA 0 1 64.173
161300707 GT-AG 0 1.000000099473604e-05 110 rna-XM_024593900.1 28932359 4 26414601 26414710 Populus trichocarpa 3694 AAG|GTCTGAATTT...TTATTCTGAATA/ATTATTCTGAAT...TGCAG|CTG 1 1 69.434
161300708 GT-AG 0 0.0001826185777628 192 rna-XM_024593900.1 28932359 5 26414836 26415027 Populus trichocarpa 3694 CAG|GTATGGTGCT...TTCCTTTTAACT/TTTATTTTAATT...TCCAG|GTT 0 1 71.709
161300709 GT-AG 0 0.0008085054845624 176 rna-XM_024593900.1 28932359 6 26415489 26415664 Populus trichocarpa 3694 CAG|GTAACTTAAT...ATTTCCTTTTTT/ATTTGTTTCATG...GACAG|GGA 2 1 80.102
161300710 GT-AG 0 1.000000099473604e-05 110 rna-XM_024593900.1 28932359 7 26415694 26415803 Populus trichocarpa 3694 AGG|GTGAGCAGTT...TGTATCTTACAA/TTGTATCTTACA...TACAG|GAT 1 1 80.63
161300711 GT-AG 0 0.0044929493371697 173 rna-XM_024593900.1 28932359 8 26416434 26416606 Populus trichocarpa 3694 GAG|GTAACTATGT...ATTTTTTTATTT/TATTTTTTTATT...TGCAG|AGT 1 1 92.099

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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]);