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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAAATGCATGTTAAAAGGGGCAGTTGATTTTCTTATAAAACCCATTCGGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcatattttcagtcctgtttaaagagataattttttgtatttttttttcttcttttatcttggcttgctattttagcgtatatttacttattctttctatcctctctgctgtataatatttattcag

Basic information

species Glycine max
transcript GLYMA07G05530.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05530.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv15s0048g02540.t01 (Vitis vinifera), 5'ss of exon 3
ATTGAAATGCATGTTAAAAGGGGCAGTTGATTTTCTTATAAAACCCATTCGGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcatattt--tcagtcctgtttaaagagataattttttgtatttttttttcttcttttatcttggcttgctattttagcgtatatttacttattctttctatcctctctgctgtataatatttattcag
 |||||||||||||| |||||||| | ||| |||||| | || ||  || ||||||||||||| |||||| | ||||| ||||| ||||||||||| || ||| ||   ||||  ||| |  |  ||    ||  | |  || | |||  |    | | |  ||  |||  ||    ||| |    |  || ||| ||| ||||  |  | | |  | ||    ||||  ||||
TTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAACCTATGGCAGCATGTTTGGAGAAGGCATGCAgtaagtttaatttgctcaattttccttctccag-cattggttgggattgct---ccgtttcctagtttgattt---ttttcacacaactttcactgattttttccttaatattt-tttta----attttctcag
















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|207809370|gb|GD782676.1|GD782676
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCA
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCA
EST: gi|193384245|gb|FK349299.1|FK349299
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAA-CTTAAAACT
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAAACTTAAAACT
EST: gi|208323744|gb|GE122315.1|GE122315
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAGGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTCTTCACCGAAAAA
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAA
EST: gi|213595702|gb|DB962474.1|DB962474
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCACCG
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACCG
EST: gi|208332607|gb|GE130272.1|GE130272
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCACC
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACC
EST: gi|209726010|gb|BW654795.1|BW654795
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAAACTTAAAACT
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAAACTTAAAACT
EST: gi|193371412|gb|FK336925.1|FK336925
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAAATACAACCTTTTCA
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAA-TACAACCTTTTCA
EST: gi|208269240|gb|GE070248.1|GE070248
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAA-CTTAAA
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAAACTTAAA
EST: gi|208167545|gb|GD965169.1|GD965169
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAAACTTAAAACT
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAAACTTAAAACT
EST: gi|18734852|gb|BM528422.1|BM528422
EST:     GCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAAACTTAAAACT
genomic: GCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACCGAAAAAACTTAAAACT
EST: gi|208187444|gb|GD985474.1|GD985474
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCAC
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCAC
EST: gi|207818832|gb|GD790303.1|GD790303
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCACCG
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCACCG
EST: gi|193418967|gb|FK382253.1|FK382253
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTT
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTT
EST: gi|193341542|gb|FK306754.1|FK306754
EST:     GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCT                         ATTAGCACTCCTACTCAAAATACAACCTTTTCA
genomic: GGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcata ... atttattcagATTAGCACTCCTACTCAAAATACAACCTTTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGAAATGCATGTTAAAAGGGGCAGTTGATTTTCTTATAAAACCCATTCGGAAGAATGAGCTTAGGAACTTGTGGCAACATGTATGGAGAAGGCACGCTgtatgtcatattttcagtcctgtttaaagagataattttttgtatttttttttcttcttttatcttggcttgctattttagcgtatatttacttattctttctatcctctctgctgtataatatttattcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA