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 = 38490423

✎ View and edit SQL

This data as json, CSV (advanced)

Suggested facets: score, phase, in_cds

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
213116227 GT-AG 0 0.0456465260945682 118 rna-XM_008654421.3 38490423 2 25899370 25899487 Zea mays 4577 GAG|GTATGCTCCT...ACGTTCTTATTC/TTCTTATTCATG...TGTAG|AAA 0 1 50.464
213116228 GT-AG 0 0.0018913391451998 509 rna-XM_008654421.3 38490423 3 25899607 25900115 Zea mays 4577 CAG|GTACTCCCTA...CTAATCTTAATG/AATGTTTTCATA...TGTAG|TCA 2 1 52.863
213116229 GT-AG 0 3.003719099734109e-05 165 rna-XM_008654421.3 38490423 4 25901829 25901993 Zea mays 4577 CAG|GTAAACATCA...AAAACCTTTATT/ATGTTGCTTACA...CACAG|CAC 2 1 87.399
213116230 GT-AG 0 1.000000099473604e-05 90 rna-XM_008654421.3 38490423 5 25902043 25902132 Zea mays 4577 AAG|GTTAGTACAA...TTTATCTTGATG/TTTATCTTGATG...AACAG|GAT 0 1 88.387
213116231 GT-AG 0 3.510534925012941e-05 137 rna-XM_008654421.3 38490423 6 25902375 25902511 Zea mays 4577 TAA|GTAAGTCTTT...ACATCCTTGTTG/ATTTTACTGATT...ACTAG|CCC 2 1 93.266
213116232 GT-AG 0 0.0012540430421331 1042 rna-XM_008654421.3 38490423 7 25902617 25903658 Zea mays 4577 AAG|GTATGCAATG...GCCTCCTTTTCG/TTTCGGTTGAAA...TACAG|TTT 2 1 95.383
213136400 GT-AG 0 1.000000099473604e-05 1639 rna-XM_008654421.3 38490423 1 25895314 25896952 Zea mays 4577 GAG|GTAGGTCTCG...ACATACTTATTT/TACATACTTATT...TGCAG|TCT   0 6.069

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]);