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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC

Basic information

species Glycine max
transcript GLYMA18G44210.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 8
gtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggt-ttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
                 |  || ||||  |  |      || |   |||  |   |  ||  | |  || | || | |  || ||| |  | |||     |||| ||      | ||   |  | ||| |   |||    |||||   ||                    ||||  ||| |||||||||| ||||| |||||||||||||| || |||||||| ||||| |||||| | |||||||| ||||| ||| | ||||| |||||||
----------------gtgctattaaccgtctttgctttttttgaatgatctaatactttggacatcaacattttgtt--ggcattgttatgttgtttgagaattatcacttcagtacc-atcactttgttcatttc---cttactcaaa-------------------ccagCCGAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTC

upper sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatactaa--ggaatattttataagttttgagcttacctgaagaagtatgtggttgttcttt---cagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
                                                                                     | || |||| | |  | ||    |  |  |||  | |  ||||  || | | |  |  |   |||  | |  |||   | | ||||    |||  ||| |||||||||| |||||  ||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||||||||||| ||||| |||||||
------------------------------------------------------------------------------------gtttgttttgtccattattatatttccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC

upper sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 9
gtgtctggattatttt---tttgtaata-actctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
  ||    |||   ||   |||||  || ||  | ||| |    |  || ||   |||  |    | |   ||  |     ||  |||        | | |     |  |  |  |  |    |  || | ||| |    |     || |  |    |||    |  || |||||||  ||| | || ||||| |||||| |||| || |||||||||||||| || ||||| || ||||| ||||||||||||||||||||||| || |||||||
--gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacc------tagaagaatgttgtgctggtttt----atcatctcatatgcccagttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC

upper sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggct-aaggtattctggtttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
                                                                        ||| ||  | || |  | ||||         ||||  |  |   || |    |   ||   | | ||   ||| |  |    | | |  || || || |||| |||| | |||||||| ||||| |||||||| ||||| || ||| | |||||||||||||| |  ||||| |||||||||||| | ||||| ||||| |
----------------------------------------------------------------------tgttgtcttgatgtttctttgtttttatccatgtaatttttttttgaatgctagtagcattc-tctggatactactt--actgttttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC

upper sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
                                          ||| |    || || |||   | |||  | ||   ||        |  ||  |     |  | ||| ||   | |          | |||  ||||  ||             |    ||  | || |||| |||| | |||||||| ||||| |||||||| || ||||| ||||| || ||||||||||||   ||||| ||||| |||||  | ||||| |||||||
------------------------------------------tttttcgtttttaaaattt--ttatatcatttaatta-------ttatttgtgtcgaaatcagtagcaaatttgaaa--------acaagacttgatttt-------------tagcctttctattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCTTTCGAGGTGTGGCTGGAGCATGGTTCTGAAAGGAAGAAGCCACCTGAGCAACTTCCTATCGTTCTTC

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|6916382|gb|AW397912.1|AW397912
EST:     GCCTCTCTCAACTTCCATCTTTAGTTGAGGATCCTAATTCTGAATATCAG                         CGTAGTACATGTGTCACCGAGCAGGTGACAGCATTTGAAGTATGG
genomic: GCCTCTCTCAACTTCCATCTTTAGTTGAGGATCCTAATTCTGAATTTCAGgtgtctggat ... gttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC
                    agcttac  putative branch site (score: 3)
                                           ttgttctttc  putative PPT
     attttataagttttga  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcagCGTAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG