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 = 28932426

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Suggested facets: dinucleotide_pair, score, phase, in_cds

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
161301596 GT-AG 0 9.797007572066905e-05 732 rna-XM_024585273.1 28932426 2 29184921 29185652 Populus trichocarpa 3694 GAG|GTATGATTGG...ACTTCTGTATTT/CTGTATTTCACG...TGCAG|TGC 0 1 18.945
161301597 GT-AG 0 1.000000099473604e-05 82 rna-XM_024585273.1 28932426 3 29185779 29185860 Populus trichocarpa 3694 CAG|GTGAGCGAGG...GCTATCTTCTCT/CTGAAGTTGATT...CGCAG|GAC 0 1 22.065
161301598 GT-AG 0 4.113482932572017 192 rna-XM_024585273.1 28932426 4 29186059 29186250 Populus trichocarpa 3694 AAG|GTATCTTACT...TGTCTCTTGATC/TGTCTCTTGATC...TGCAG|TTG 0 1 26.969
161301599 GT-AG 0 1.000000099473604e-05 96 rna-XM_024585273.1 28932426 5 29186479 29186574 Populus trichocarpa 3694 AAG|GTGACTCTTT...AAGGTTTTATAT/TTTATATTTACT...GGCAG|GAA 0 1 32.615
161301600 GT-AG 0 0.0020687596080575 432 rna-XM_024585273.1 28932426 6 29187697 29188128 Populus trichocarpa 3694 GAG|GTAAACTTTG...AATGTTTTAATG/AATGTTTTAATG...TGCAG|GAA 0 1 60.401
161301601 GT-AG 0 1.000000099473604e-05 448 rna-XM_024585273.1 28932426 7 29188417 29188864 Populus trichocarpa 3694 CAG|GTGTGTGTAG...TTCCCATTATCA/ATGATATTAACT...TGTAG|GTT 0 1 67.533
161301602 GC-AG 0 1.000000099473604e-05 393 rna-XM_024585273.1 28932426 9 29189317 29189709 Populus trichocarpa 3694 CAG|GCAAGTAATT...TATTTCTAATTT/TTATTTCTAATT...TACAG|CTG 1 1 78.702
161317269 GT-AG 0 0.0001978523709508 443 rna-XM_024585273.1 28932426 1 29183820 29184262 Populus trichocarpa 3694 CAG|GTAACACTTA...TTTTACTTATTC/GTTTTACTTATT...TACAG|TTT   0 3.418

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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]);