Databases available for BLAST search
Nucleotide Sequence Databases
- EST_contigs : 24,713 sequences
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Assembled EST sequences
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EST_clones : 93,692 sequences
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Individual EST sequences from the five cDNA libraries.
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1: JMFF library: 34,200 sequences
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JMSF stands for Japanese Morning glory Flower Full-length. The cDNAs were synthesized by CAP trapper method from mRNA isolated from flowers and flower buds. Both 5' and 3' ends were sequenced, and the names of the 3' end sequence were prefixed with "r". The numbers of 5' (JMFF) and 3' (rJMFF) sequences are 17,254 and 16,946, respectively.
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2: JMFS library: 36,341 sequence
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JMFS stands for Japanese Morning glory Flower Size-selected. The cDNA fragments with over 3 kb long were fractionated. Total RNA was extracted from flowers and flower buds, and mRNA was purified. Both 5' and 3' ends were sequenced, and the names of the 3' end sequence were prefixed with "r". The numbers of 5' (JMFS) and 3' (rJMFS) sequences are 18,627 and 17,714, respectively.
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3: JMFN library: 9,012 sequences
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JMFN stands for Japanese Morning glory Flower Normalized. The cDNA fragments with 0.5 - 3 kb long were collected and normalized. Total RNA was extracted from flowers and flower buds.
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4: JMSF library: 13,068 sequences
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JMSF stands for Japanese Morning glory Seedling Full-length. The cDNAs were synthesized by CAP trapper method from mRNA isolated from aerial part of seedlings at 8 days after seeding.
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5: JMCP library: 1,071 sequences
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JMCP stands for Japanese Morning glory seed Coat PCR. It was made from mRNA extracted from seed coats using a SMART cDNA Library Construction Kit (Clontech).
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asagao_genome : 3,416 sequences
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The latest scaffold sequences of the draft genome. The sequences of scaffold0001-scaffold3416 are available from accession numbers BDFN01000001-BDFN01003416.
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predicted_CDS : 44,916 sequences
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The coding sequences deduced from 44,916 predicted_transcripts.
- predicted_transcripts : 44,916 sequences
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The predicted transcripts derived from 42,783 gene models on the draft genome.
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asagao_genome_old : 3,512 sequences
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The scaffold sequences of the draft genome.
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predicted_CDS_old : 43,397 sequences
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The coding sequences deduced from 43,397 predicted_transcripts.
- predicted_transcripts_old : 43,397 sequences
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The predicted transcripts derived from 43,008 gene models on the draft genome.
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BAC_clones : 46,848 sequences
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End sequences of 23,424 BAC clones in JMHiBa library. JMHiBa stands for Japanese Morning glory HindIII BAC. Genomic DNA from TKS was digested with HindIII, and was cloned into pIndigoBAC536.
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RNA-seq assembled : 163,898 sequences
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RNA-seq from six tissues including leaf, flower, stem, root, embryo, and seed coat was assembled using Trinity. N50 and average lengths are 1,337 bp and 567 bp, respectively.
- DEG seed coat : 271 sequences
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Differentially Expressed Genes in seed coat.
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DEG embryo : 218 sequences
- Differentially Expressed Genes in embryo.
- DEG root : 414 sequences
- Differentially Expressed Genes in root.
- DEG stem : 108 sequences
- Differentially Expressed Genes in stem.
- DEG leaf : 284 sequences
- Differentially Expressed Genes in leaf.
- DEG flower : 488 sequences
- Differentially Expressed Genes in flower.
- Africa : 1,007 sequences
- Unpublished de novo sequences of Q0063 (AKX084, 2013012).
sum = 737079967, n = 1007, ave = 731956.27, largest = 7622810
N50 = 1616267, n = 126
- Violet : 1,265 sequences
- Unpublished de novo sequences of Violet (AKX227, 2020267-8).
sum = 772125942, n = 1265, ave = 610376.24, largest = 12469579
N50 = 2384516, n = 90
- Q531 : 919 sequences
- Unpublished de novo sequences of Q531 (AK138, 2016010).
sum = 751712942, n = 919, ave = 817968.38, largest = 10651820
N50 = 2268820, n = 94
- Tokyo Kokei Standard New: 1,155 sequences
- Genomic DNA was extracted from the individual used for the first draft genome sequence (Hoshino et al., 2016).
sum = 766549086, n = 1155, ave = 663678.86, largest = 11768992
N50 = 2105324, n = 106