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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGGGATGCTTGCTGGTGAAATGAAGCATGGTCCTTTGGCATTAGTGGATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtgactgtcgagtagctttattatctgaaattaggagtttgatattgacatattttatctttgacag

Basic information

species Glycine max
transcript GLYMA09G38460.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38460.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 9
GTGAAGGGATGCTTGCTGGTGAAATGAAGCATGGTCCTTTGGCATTAGTGGATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgt-------gactgtcgagtagctttattatctgaaa-----ttaggagtttgatattgacatattttatctttgacag
| ||||| |||||||||||||||||||||||||| ||  | ||| ||||||||||||| || || ||    ||  | ||||| |||||||| ||||||||||  |   |       |||||  ||| |  || ||| |||         | | |   ||  | |  ||||  || | || |  |||
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacat-cttcacctcttgcag

upper sequence: GLYMA09G38460.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 9
GTGAAGGGATGCTTGCTGGTGAAATGAAGCATGGTCCTTTGGCATTAGTGGATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgt-------gactgtcgagtagctttattatctgaaa-----ttaggagtttgatattgacatattttatctttgacag
| ||||| |||||||||||||||||||||||||| ||  | ||| ||||||||||||| || || ||    ||  | ||||| |||||||| ||||||||||  |   |       ||||   ||| |  || ||| |||         | | |   ||  | |  ||||  || | || |  |||
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacat-cttcacctcttgcag
















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|298174671|gb|HO014702.1|HO014702
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
EST: gi|207813117|gb|GD783707.1|GD783707
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAG
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAG
EST: gi|207768257|gb|GD739941.1|GD739941
EST:     GCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
EST: gi|192325841|gb|FK018063.1|FK018063
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
EST: gi|58025101|gb|CX711842.1|CX711842
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
EST: gi|193468008|gb|FK434003.1|FK434003
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGGAACTTAATGCC
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCC
EST: gi|209696471|gb|BW664020.1|BW664020
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAGGGATGCTTGCTGGTGAAATGAAGCATGGTCCTTTGGCATTAGTGGATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtgactgtcgagtagctttattatctgaaattaggagtttgatattgacatattttatctttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT