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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGATATTCGTGAAAACCCTAACCGGGAAGACCATCACCCTTGAGGTGGAGTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttgatccacgattgattggttatcgttctctgtttttcgctcttgtttgattcatttttgtttttttctaattgcctag

Basic information

species Glycine max
transcript GLYMA04G40980.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40980.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os09g39500.1 (Oryza sativa), 5'ss of exon 1
CAGATATTCGTGAAAACCCTAACCGGGAAGACCATCACCCTTGAGGTGGAGTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttgatccacgattgattggttatcgttctctgtttttcgctc---ttgtttgattcatttttgtttttttctaattgcctag-----------
||||| |||||||| |||||||| |||||||||||||| || ||||| |||   ||||||||||| ||||||||||| |||||||| |||||||| |||||| ||||| | |   |  ||         || |  |||  || | ||||    | |||       ||   |     || |  |||   |           
CAGATCTTCGTGAAGACCCTAACGGGGAAGACCATCACGCTCGAGGTCGAGAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAGGACAAGGAAGgtacgctt-gcttagcatttagcaatgcttcttcttcttcttcttgctcggtctcttttgcctgcttgattgcgaatcgatctgctccgcggggcctcag
















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|57574197|gb|CX547172.1|CX547172
EST:     GGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|151398433|gb|EV268304.1|EV268304
EST:     GTCAAGCGACACCATCGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|13240099|gb|BG359408.1|BG359408
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|208281706|gb|GE073784.1|GE073784
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|151410135|gb|EV279943.1|EV279943
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|18719025|gb|BM523129.1|BM523129
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|192324803|gb|FK016874.1|FK016874
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|213618032|gb|DB963665.1|DB963665
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|192317237|gb|FK009810.1|FK009810
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAAATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|58023032|gb|CX709773.1|CX709773
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|57574032|gb|CX547007.1|CX547007
EST:     GGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGTTGGAAG
genomic: GGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
EST: gi|151412758|gb|EV282570.1|EV282570
EST:     GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAG                         GGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG
genomic: GTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttg ... aattgcctagGGATTCCTCCGGATCAGCAGAGGTTGATCTTCGCCGGTAAACAGCTGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGATATTCGTGAAAACCCTAACCGGGAAGACCATCACCCTTGAGGTGGAGTCAAGCGACACCATTGACAATGTCAAAGCCAAGATTCAGGACAAAGAAGgttcgctttgatccacgattgattggttatcgttctctgtttttcgctcttgtttgattcatttttgtttttttctaattgcctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG