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)

10 rows where transcript_id = 20781793

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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
111341623 GT-AG 0 1.000000099473604e-05 815 rna-XM_043955185.1 20781793 1 13949741 13950555 Manihot esculenta 3983 TTG|GTGAGATTAG...GTGTTCTTGTTT/CATTATTTGATT...TCAAG|TAC 2 1 1.761
111341624 GT-AG 0 1.000000099473604e-05 6313 rna-XM_043955185.1 20781793 2 13943280 13949592 Manihot esculenta 3983 GAG|GTTTGGTTCC...GGTTCAATGATC/AGAAGGTTCAAT...TAAAG|ATG 0 1 5.594
111341625 GT-AG 0 1.000000099473604e-05 459 rna-XM_043955185.1 20781793 3 13941597 13942055 Manihot esculenta 3983 CGT|GTCATTCATG...TTTTTCTAAGTT/CTTTTTCTAAGT...TGCAG|GAG 0 1 37.296
111341626 GC-AG 0 0.0003410655300598 447 rna-XM_043955185.1 20781793 4 13940903 13941349 Manihot esculenta 3983 TGC|GCATGTGTGT...GTAATCTTAAGA/TTTGTACTGATA...CCTAG|GAT 1 1 43.693
111341627 TT-TT 0 0.0096056609081208 132 rna-XM_043955185.1 20781793 5 13940137 13940268 Manihot esculenta 3983 ACG|TTATGCATTG...ATGTATTTAAGG/GATGTATTTAAG...TATTT|GCA 2 1 60.114
111341628 AC-GG 0 1.000000099473604e-05 153 rna-XM_043955185.1 20781793 6 13939211 13939363 Manihot esculenta 3983 TGA|ACGAGTTGTC...AAAGTTGTATTC/GTTGTATTCAAA...TTGGG|TTT 1 1 80.135
111341629 GT-AG 0 1.000000099473604e-05 54 rna-XM_043955185.1 20781793 7 13939022 13939075 Manihot esculenta 3983 TTG|GTGTAAGTGC...CTACCTTTAATG/ATGTTTCTGATT...TACAG|ATT 1 1 83.631
111341630 GC-AG 0 1.000000099473604e-05 56074 rna-XM_043955185.1 20781793 8 13882823 13938896 Manihot esculenta 3983 GAA|GCACTTCAAG...TAATTGTTGAAT/AGCGATTTAATT...TGAAG|GTT 0 1 86.869
111341631 GT-AG 0 1.000000099473604e-05 2988 rna-XM_043955185.1 20781793 9 13879756 13882743 Manihot esculenta 3983 ACG|GTTAGCTAGA...TTGTTCTTTGTT/TTATTTCTAACA...TTAAG|GCA 1 1 88.915
111341632 GT-AG 0 1.000000099473604e-05 3390 rna-XM_043955185.1 20781793 10 13876281 13879670 Manihot esculenta 3983 AAA|GTCAGTTGGT...TGTTTCTTGTAA/CAAGGACTGAAG...ATCAG|TAA 2 1 91.116

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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]);