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)

9 rows where transcript_id = 28932390

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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
161301149 GT-AG 0 1.000000099473604e-05 168 rna-XM_006369933.2 28932390 1 37463804 37463971 Populus trichocarpa 3694 AAG|GTGAAACATG...ATTTGTTTAATT/ATTTGTTTAATT...GACAG|GAA 0 1 53.574
161301150 GT-AG 0 1.000000099473604e-05 90 rna-XM_006369933.2 28932390 2 37463627 37463716 Populus trichocarpa 3694 TTG|GTGAGCAATA...CATTATTTGATT/CATTATTTGATT...GTTAG|GTA 0 1 55.511
161301151 GT-AG 0 0.000128894015307 104 rna-XM_006369933.2 28932390 3 37462911 37463014 Populus trichocarpa 3694 AGA|GTAAGCAATT...TTCACTTTATTG/ATTAGTTTCACT...TATAG|GTT 0 1 69.138
161301152 GT-AG 0 0.0003027837928906 222 rna-XM_006369933.2 28932390 4 37462524 37462745 Populus trichocarpa 3694 CAG|GTAATCCTTG...ATTTCCATAATG/GTTTTATTAATT...CGCAG|AGA 0 1 72.812
161301153 GT-AG 0 0.000241231510273 105 rna-XM_006369933.2 28932390 5 37462127 37462231 Populus trichocarpa 3694 CAG|GTATGTAGTT...ATACCCTTTTCC/TGTTTTCCCATT...TAAAG|CCA 1 1 79.314
161301154 GT-AG 0 0.0027900587321107 74 rna-XM_006369933.2 28932390 6 37461838 37461911 Populus trichocarpa 3694 CAG|GTAACTTTAG...TTATTATTAAAT/TTATTATTAAAT...TACAG|GTC 0 1 84.102
161301155 GT-AG 0 1.2102629675454886e-05 180 rna-XM_006369933.2 28932390 7 37461352 37461531 Populus trichocarpa 3694 GAG|GTGTGTTGTT...TGGTCATTGATG/CACATGCTAACT...TCTAG|GCT 0 1 90.915
161301156 GT-AG 0 3.8987409946094274e-05 107 rna-XM_006369933.2 28932390 8 37461181 37461287 Populus trichocarpa 3694 CAG|GTTTTTCTTT...ATTTACTTACAT/AATTTACTTACA...TGTAG|TCA 1 1 92.34
161301157 GT-AG 0 1.000000099473604e-05 90 rna-XM_006369933.2 28932390 9 37460851 37460940 Populus trichocarpa 3694 ACG|GTGCGTATTG...TTTTCTTTATTA/ATTTTCTTTATT...TGCAG|GGC 1 1 97.684

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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]);