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)

5 rows where transcript_id = 24633830

✎ View and edit SQL

This data as json, CSV (advanced)

Suggested facets: phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
134640332 GT-AG 0 4.863799680550214e-05 50 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA5073 24633830 1 478 527 Olpidium bornovanus 278681 GCC|GTATGACAGC...GGTGTCGTCGCG/TCGTCGCGGAAC...AAAAG|GCC 0 1 12.403
134640333 GT-AG 0 3.034093374516843e-05 216 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA5073 24633830 2 972 1187 Olpidium bornovanus 278681 GCC|GTTCTTCTCA...GGCTTCTGCAAA/GGAATGCGAACT...GGTAG|TCG 0 1 31.525
134640334 GT-AG 0 0.1148996198616183 57 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA5073 24633830 3 1444 1500 Olpidium bornovanus 278681 TAC|GTATGTTAGG...CCATTCTTGACT/CCATTCTTGACT...TGCAG|AAT 1 1 42.55
134640335 GT-AG 0 1.000000099473604e-05 74 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA5073 24633830 4 2295 2368 Olpidium bornovanus 278681 AAG|GTAGTTGATT...GCCGTTTTAAGC/GCCGTTTTAAGC...CTTAG|CAC 0 1 76.744
134640336 GT-AG 0 6.944165118907402e-05 115 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA5073 24633830 5 2610 2724 Olpidium bornovanus 278681 TTA|GTTTAGCGTA...AATCACTTAACT/TTTGCAATCACT...TTTAG|GTT 1 1 87.123

Advanced export

JSON shape: default, array, newline-delimited, object

CSV options: 

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]);