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)

6 rows where transcript_id = 38421858

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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
212703483 GT-AG 0 1.000000099473604e-05 1306 rna-gnl|WGS:VZUH|XIPELE_R02830_mrna 38421858 1 630735 632040 Xiphorhynchus elegans 269412 CAG|GTAAGTGAGG...GTGTTTTTGGTT/TGTGAAGTAATT...TCCAG|GGG 0 1 19.318
212703484 GT-AG 0 1.000000099473604e-05 1230 rna-gnl|WGS:VZUH|XIPELE_R02830_mrna 38421858 2 632152 633381 Xiphorhynchus elegans 269412 CAT|GTGAGTACCT...AAGCCTTTGATT/ATCTGATTTATC...TCTAG|GCA 0 1 29.83
212703485 GT-AG 0 1.000000099473604e-05 884 rna-gnl|WGS:VZUH|XIPELE_R02830_mrna 38421858 3 633467 634350 Xiphorhynchus elegans 269412 CAG|GTAAAGACTT...CAAACCATAATC/TACAATCTGATC...TGCAG|ACT 1 1 37.879
212703486 GT-AG 0 1.000000099473604e-05 284 rna-gnl|WGS:VZUH|XIPELE_R02830_mrna 38421858 4 634515 634798 Xiphorhynchus elegans 269412 CAG|GTAATTGCTA...TTTTCCTCTTTT/TGCAGTTTCACA...ATCAG|TAT 0 1 53.409
212703487 GT-AG 0 1.6598982057433e-05 798 rna-gnl|WGS:VZUH|XIPELE_R02830_mrna 38421858 5 634913 635710 Xiphorhynchus elegans 269412 TCT|GTGAGTATGC...TTTCTCTTGACT/TGTTTTCTAACT...GCCAG|AAT 0 1 64.205
212703488 GT-AG 0 0.000325639239399 820 rna-gnl|WGS:VZUH|XIPELE_R02830_mrna 38421858 6 635841 636660 Xiphorhynchus elegans 269412 CTA|GTACTGTTAC...TTTTTTTTTCCA/CCTGGAGTTACC...TCCAG|GTC 1 1 76.515

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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]);