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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAGGGCAGAGTCCATGGTATGATAATCTCTGCAGACCTGTTACAGACCTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataatatttttcttttcttttctttgggtattgttctccgtgtgtagatattgctaataatgctgaaatcaaaaccaattgatgttttaaacacttattctgatttgtaacatcttgctttaataaattggatgttactactctaacctgctgtctgtatatgtgattgca

Basic information

species Glycine max
transcript GLYMA18G53700.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G53700.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 5'ss of exon 2
AAGAAGGGCAGAGTCCATGGTATGATAATCTCTGCAGACCTGTTACAGACCTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataatat-----ttttcttttcttttctttgggtattgttctccgtgtgtagatattgctaataatgctgaaatcaaaaccaattgatgttttaaacacttattctgatttgtaacatcttgctttaataaattggatgttactactctaacctgctgtctgtatatgtgattgca
  | ||||||||| |||||||||||||| |||||||| |||||||| || || ||||| || || ||||||||||||||||| || ||||||||||| |||||||| | |      |||| | || || ||||||| | ||   ||        || | | |   ||| | ||      |  |  ||   | |      |                                                                                
-GGGAGGGCAGAGCCCATGGTATGATAACCTCTGCAGGCCTGTTACCGATCTCCTTCCACTGATTGCAAGTGGTGTCAGAGGTGTAACTAGCAACCCAGCGgtaattacacataccttttttcttattctctttggttcttcccctgttccaacaggtgtggaggatatttcttttgatagtagaaaggaaagagggggaa-------------------------------------------------------------------------------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|7233907|gb|AW569249.1|AW569249
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|6566822|gb|AW234454.1|AW234454
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|12689429|gb|BG155826.1|BG155826
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|213592579|gb|DB961839.1|DB961839
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|213593697|gb|DB971719.1|DB971719
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|7233788|gb|AW569131.1|AW569131
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|21887135|gb|BQ740348.1|BQ740348
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|254318817|gb|GR830381.1|GR830381
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|6913943|gb|AW395473.1|AW395473
EST:     CTGCTTGCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTGTGAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGGTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|18721154|gb|BM523327.1|BM523327
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|298174178|gb|HO017514.1|HO017514
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAGTGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|7924409|gb|AW830435.1|AW830435
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|24136489|gb|BU926999.1|BU926999
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
EST: gi|24205422|gb|BU964675.1|BU964675
EST:     CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGC                         GATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA
genomic: CTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataata ... tgtgattgcaGATCTTTCAGAAAGCTATCTCATCATCGAATGCTTACAATGATCAGTTCA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAAGGGCAGAGTCCATGGTATGATAATCTCTGCAGACCTGTTACAGACCTGCTTCCTCTTATAGCAAGTGGTGTCAGAGGCGTCACTAGCAACCCTGCggtaataatatttttcttttcttttctttgggtattgttctccgtgtgtagatattgctaataatgctgaaatcaaaaccaattgatgttttaaacacttattctgatttgtaacatcttgctttaataaattggatgttactactctaacctgctgtctgtatatgtgattgca

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