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 = 5963408

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Suggested facets: dinucleotide_pair, score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
30552743 GC-AG 0 1.000000099473604e-05 90 rna-XM_042346908.1 5963408 1 99558576 99558665 Callorhinchus milii 7868 GCA|GCCGGTGCCG...ACCTCTATGGCT/GCGCCGCTCACC...AAAAG|CAA 2 1 17.633
30552744 GT-AG 0 0.0017748824715255 21266 rna-XM_042346908.1 5963408 2 99537120 99558385 Callorhinchus milii 7868 AAG|GTAACCCACC...TAGACGTTGATG/TTGATGGTAATG...CTCAG|GTT 0 1 21.67
30552745 GT-AG 0 1.000000099473604e-05 32135 rna-XM_042346908.1 5963408 3 99504735 99536869 Callorhinchus milii 7868 AAG|GTAAGACATC...GTATTTTTATTC/TGTATTTTTATT...TGCAG|GTG 1 1 26.981
30552746 GT-AG 0 1.000000099473604e-05 481 rna-XM_042346908.1 5963408 4 99504166 99504646 Callorhinchus milii 7868 TAG|GTAAGGGAAC...GAGTCCTAAAAT/CCGGTTTTGAGT...CCTAG|GTT 2 1 28.851
30552747 GT-AG 0 1.632252046827906e-05 2485 rna-XM_042346908.1 5963408 5 99499175 99501659 Callorhinchus milii 7868 CAG|GTATGTGATT...AAAACTGTGACT/CGTGTTGTAATT...CGTAG|GAG 0 1 82.091
30552748 GT-AG 0 1.000000099473604e-05 528 rna-XM_042346908.1 5963408 6 99498223 99498750 Callorhinchus milii 7868 CAG|GTACGTGCTT...AAGGCTTCAACT/TCAACTCTCATC...CTCAG|GGG 1 1 91.098
30552749 GT-AG 0 1.000000099473604e-05 1303 rna-XM_042346908.1 5963408 7 99496747 99498049 Callorhinchus milii 7868 GGG|GTAAGTAGGG...TTTTTTTTGCCT/CAATTCCTAATG...TGTAG|CCG 0 1 94.774
30552750 GT-AG 0 1.000000099473604e-05 1899 rna-XM_042346908.1 5963408 8 99494688 99496586 Callorhinchus milii 7868 AAG|GTACTAACTC...GAAGTTTTAACC/CCTTTCTTCAAT...CTCAG|GGC 1 1 98.173

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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]);