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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTACCGTGGAGATTTGGCCGTCAAAGTGTTCTCAATGCCCTTAAAGATTCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTGgtcagtactttatgagcctgttgaatgatattattttatccaataacactttgttgataatgtaatttcctgcttttcag

Basic information

species Glycine max
transcript GLYMA08G41630.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G41630.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G06690.1 (Arabidopsis thaliana), 5'ss of exon 4
CACTACCGTGGAGATTTGGCCGTCAAAGTGTTCTCAATGCCCTTAAAGATTCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTGgtcagtactttatgagcctgttgaatgatattattttatccaataacactttgttgataatgtaatttcctgcttttcag
|| | || ||| ||||||| ||| |||||||| ||| ||||||||||||||||||||  || || |  ||  | || || ||||| ||||| || |||||||  | ||        | ||||| |  | |  |   ||     ||||| |    | |  || |  ||   |   ||||||
CATTGCCATGGCGATTTGGTCGTGAAAGTGTTGTCACTGCCCTTAAAGATTCCCTTTCCCGGCTTGAGCTTTCATCTGTTGATCTCTATCAACTGCATTGgtatgcacccctaattcatgttggagtaaacaacactagaaggtaacaatc---tcactattttcttaattatatttcag

upper sequence: GLYMA08G41630.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv12s0028g01100.t01 (Vitis vinifera), 5'ss of exon 4
CACTACCGTGGAGATTTGGCCGTCAAAGTGTTCTCAATGCCCTTAAAGATTCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTGgtcagtactttatgagcctgttgaatgatatt-------attttatccaataacactttgttgat-aatgtaatt-tcctgcttttcag
|  |||| ||||| ||||| ||||| |||||  ||| ||||||||| |||||||| ||||| || |||||    ||||||||||| ||||| |||||||||||||| |||||||||||| |  | |   ||         |||    |||  | |  | | | || || ||   | | |   |||||||
CTTTACCATGGAGGTTTGGACGTCAGAGTGTAATCACTGCCCTTAAGGATTCCCTATGTCGCCTTGGACTTTTGTCAGTGGATCTCTATCAACTTCATTGgtcagtgctttatgagcctttatactaccatctatctgagtttctgtcaaagaaaaatagctaatcaaagtgtctgtaccaattttcag
















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|209701051|gb|BW652163.1|BW652163
EST:     TCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTG                         GCCTGGAGTTTGGGGAAATGAAG
genomic: TCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTGgtcagtactt ... tgcttttcagGCCTGGAGTTTGGGGAAATGAAG
EST: gi|10231875|gb|BE800763.1|BE800763
EST:     TCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTG                         GCCTGGAGTTTGGGGAAATGAAG
genomic: TCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTGgtcagtactt ... tgcttttcagGCCTGGAGTTTGGGGAAATGAAG
EST: gi|22524681|gb|BU083492.1|BU083492
EST:     TCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTG                         GCCTGGAGTTTGGGGAAATGAAG
genomic: TCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTGgtcagtactt ... tgcttttcagGCCTGGAGTTTGGGGAAATGAAG
EST: gi|14205390|gb|BG839068.1|BG839068
EST:     TTTATCAGCTTCATTG                         GCCTGGAGTTT-GGGAAATGAAG
genomic: TTTATCAGCTTCATTGgtcagtactt ... tgcttttcagGCCTGGAGTTTGGGGAAATGAAG
EST: gi|9259707|gb|BE347854.1|BE347854
EST:     TCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTG                         GCCTGGAGTTTGGGGAAATGAAG
genomic: TCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTGgtcagtactt ... tgcttttcagGCCTGGAGTTTGGGGAAATGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTACCGTGGAGATTTGGCCGTCAAAGTGTTCTCAATGCCCTTAAAGATTCCCTTTGTCGACTAGGACTGACTTCAGTGGATCTTTATCAGCTTCATTGgtcagtactttatgagcctgttgaatgatattattttatccaataacactttgttgataatgtaatttcctgcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT