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 = 35543691

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id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
199804989 GT-AG 0 8.74870341511473e-05 575 rna-gnl|WGS:VXBI|TOXRED_R12612_mrna 35543691 1 945516 946090 Toxostoma redivivum 99882 CAG|GTAACTCAGC...CTCACTGTAACA/AATCCCCTCACT...CATAG|TTA 2 1 17.878
199804990 GT-AG 0 3.5991013877498924e-05 354 rna-gnl|WGS:VXBI|TOXRED_R12612_mrna 35543691 2 945026 945379 Toxostoma redivivum 99882 AAG|GTATGTGGGG...TCCTGCTTAGCA/CAGTGTCTGACC...TACAG|ACC 0 1 33.564
199804991 GT-AG 0 1.000000099473604e-05 265 rna-gnl|WGS:VXBI|TOXRED_R12612_mrna 35543691 3 944618 944882 Toxostoma redivivum 99882 AGA|GTGAGTACTG...TCTTCCTAAGTT/TTGAGTTTAACT...CTCAG|GAA 2 1 50.058
199804992 GT-AG 0 1.974385406409175e-05 1165 rna-gnl|WGS:VXBI|TOXRED_R12612_mrna 35543691 4 943368 944532 Toxostoma redivivum 99882 CAG|GTATAAAAGT...ATATCCTTGTCT/TGTCTCTTCAGC...TGCAG|GCC 0 1 59.862
199804993 GT-AG 0 1.000000099473604e-05 1178 rna-gnl|WGS:VXBI|TOXRED_R12612_mrna 35543691 5 942085 943262 Toxostoma redivivum 99882 GAT|GTGAGTCCTT...ACAGCTTTCTCT/ATTCAGGTCACA...TGCAG|TTT 0 1 71.972
199804994 GT-AG 0 0.0044287613652421 373 rna-gnl|WGS:VXBI|TOXRED_R12612_mrna 35543691 6 941556 941928 Toxostoma redivivum 99882 CAG|GTAACCTTAG...TCTCCCTGTGTC/TGCAAGTTCAGG...CCCAG|GTA 0 1 89.965
199804995 GT-AG 0 6.870976075112179e-05 1338 rna-gnl|WGS:VXBI|TOXRED_R12612_mrna 35543691 7 940164 941501 Toxostoma redivivum 99882 ACT|GTAAGTTATG...GGGCACTAAACT/GGGGCACTAAAC...CACAG|ATC 0 1 96.194

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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]);