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 = 38421853

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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
212703441 GT-AG 0 0.0044367556608984 3347 rna-gnl|WGS:VZUH|XIPELE_R11153_mrna 38421853 1 557091 560437 Xiphorhynchus elegans 269412 GTG|GTACACCTTT...AGGTTTTTATAT/AAGGTTTTTATA...TAAAG|GAT 1 1 54.864
212703442 GT-AG 0 1.844446611468737e-05 142 rna-gnl|WGS:VZUH|XIPELE_R11153_mrna 38421853 2 556843 556984 Xiphorhynchus elegans 269412 TAG|GTGTGTACCA...ATGACCTTGACT/TTTTTCTTTACC...TTTAG|AAA 2 1 61.151
212703443 GT-AG 0 1.000000099473604e-05 612 rna-gnl|WGS:VZUH|XIPELE_R11153_mrna 38421853 3 556083 556694 Xiphorhynchus elegans 269412 CAG|GTCAGAGATG...TCTTGCATAATT/TATTTACTGATT...TACAG|ATA 0 1 69.929
212703444 GT-AG 0 1.000000099473604e-05 1894 rna-gnl|WGS:VZUH|XIPELE_R11153_mrna 38421853 4 554141 556034 Xiphorhynchus elegans 269412 AAG|GTGAGGGGTT...CATTCCTCCTCT/TCTGTGCTCATT...TTTAG|GTT 0 1 72.776
212703445 GT-AG 0 29.485822669853697 3241 rna-gnl|WGS:VZUH|XIPELE_R11153_mrna 38421853 5 550822 554062 Xiphorhynchus elegans 269412 AAG|GTATCCTTTA...CTGCCTTTAGAA/TTGAGTCTAATA...TCCAG|GTG 0 1 77.402
212703446 GT-AG 0 1.000000099473604e-05 1661 rna-gnl|WGS:VZUH|XIPELE_R11153_mrna 38421853 6 549023 550683 Xiphorhynchus elegans 269412 GAG|GTAAGAGTGG...TGTTCTTTAGCT/CTGTTCTTTAGC...TAAAG|AAC 0 1 85.587
212703447 GT-AG 0 1.000000099473604e-05 1383 rna-gnl|WGS:VZUH|XIPELE_R11153_mrna 38421853 7 547556 548938 Xiphorhynchus elegans 269412 AAG|GTAATAGCAG...TGTTTCTTTTCT/AAAGATCTGACA...TTTAG|TGC 0 1 90.569
212703448 GT-AG 0 1.000000099473604e-05 90 rna-gnl|WGS:VZUH|XIPELE_R11153_mrna 38421853 8 547415 547504 Xiphorhynchus elegans 269412 CAG|GTAAGAGTAC...AGTCCTTTATTT/CTTTATTTCAAC...CCCAG|TAC 0 1 93.594

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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]);