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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag

Basic information

species Glycine max
transcript GLYMA01G36880.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 5'ss of exon 3
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag
||| |||||| | |||||  ||||||| ||||| || ||||||||| | ||||| ||||| || || ||||||||||| ||||| ||||| || || |||| |        || |||  | |  |  || |  | | | |||  |  || ||  || ||| | |||     | |||| |   |    | ||||    |||                                                                                   
TTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGTTTCAAAGAAGgcaagggact-cactttcattttctgttaataatattgatgtgctctttttttcttctttcgctaaa---gaagtttgttggtcatgtttaatttgagatcgtc-------------------------------------------------------------------------------

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 4
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggttt-ctgtatggcct--gtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag
|||||||||||||||||||||||||||||| ||||| |||||||||||  | || |||||||| || || ||||| |||||||| |||||||| || ||||||| |  | | |||  ||  | |  | |  ||||||     | | ||    |   | | |  |  || | |  ||| |||  |   ||  ||  || ||                                                                                      
TTATAACAGATTAAGACCTTTGAGTTACCGCGGTGCTGATGTTTTCATCTTAGCATTCTCTCTTATCAGTAAGGCTAGTTATGAGAATGTCTCCAAGAAGgtacgtttttgaaatgaatgtttgctacaa-gttttgatatgaatactctgaagaaagtcttttggttgtgatttttgctgctttatcttcgttttgcag--------------------------------------------------------------------------------------

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 3
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgt--acttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag
 ||||||||||||||||||||||||||||||||||| ||||||||||| || || ||||||||||| || ||||| |||||||| ||||| || || |||||    |||||   || |  | |      ||    ||  |   |     || | ||   | ||     ||| |                                                                                                                
CTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGTTTCCAAGAAGgtcagtttcgtccgaactggtcgactatttaacaattgagagttccaaattttgatgcttcttttcttttacag---------------------------------------------------------------------------------------------------------------

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 4
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag
||| |||||||| |||||||||||||| || || || |||||||||||| |||| ||||||||||| ||||||||||| ||||||||||| || || |||||       |   | ||  || | ||| | ||   ||    ||   ||| ||| | | |     |||   ||   || |  |||||   | || | |        |||  | | || | |           |||||||  |                                          
TTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGTTTCCAAGAAGgt-------gaggacttgatg-gatcaaaatgaagtga---tagcactttttagtgagtaaaggaataccaa---ttttagatggcaatttattatgtcctgggagattttttaatgtttcg-------gcttcattttcag-----------------------------------------

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 5'ss of exon 3
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag
||| |||||  |  | ||| |||||||| | ||||| ||||||||  | ||||| ||||| ||||| |||||||| |||||||||||  | || || |||||| ||  | |   ||     || ||      |  | ||  |  | | |  ||   |||   | || |   ||  |   ||   |  | | | | |                                                                                       
TTACAACAGGCTTCGTCCTCTGAGTTACAGGGGTGCTGATGTTTTTCTCCTGGCGTTCTCCCTCATCAGCAAGGCTAGTTATGAAAACATATCAAAGAAGgtatttgcttgt--ttggcattgatctcttcctactagggttgctgcgtgctagcaattgatagaagtg-gagactcacgtgaagtgtttcacgcattgcag---------------------------------------------------------------------------------

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 5'ss of exon 3
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag
||| |||||| |  ||||| | |||||| | ||||||||||| ||  ||||||| ||||||||||| |||||||| |||||||||||  ||||||| |||||| |      |   | | | ||  | || ||||||       | || |    |  ||   ||  |  |   | |   | |     |    ||| |  || | |   | | ||| | || |  |  |                                                        
TTACAACAGACTCCGACCTCTTAGTTACAGGGGTGCCGATGTGTTTTTACTGGCATTCTCTCTCATCAGCAAGGCTAGTTATGAAAACATCTCTAAGAAGgtaatagcc--cctctcagtttgtccttaatgtttt-------tatcctgaagtggatgcagacgacgagttgatacat-tgcaatcctctatgcactatct-ttactgacgttttgtgatttggcag-------------------------------------------------------

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|31455813|gb|CD397841.1|CD397841
EST:     ATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAG                         TGGATTCCGGAGTTGAAGCATGATGCTCCTGGTGTCCCCATTATTCTGGTT
genomic: ATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtg ... tcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
EST: gi|31306633|gb|CD391836.1|CD391836
EST:     ATGAAAATGTCTCTAAAAAG                         TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
genomic: ATGAAAATGTCTCTAAAAAGgtacttcgtg ... tcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
EST: gi|26268044|gb|CA819107.1|CA819107
EST:     TGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAG                         TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
genomic: TGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtg ... tcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
EST: gi|31469737|gb|CD411765.1|CD411765
EST:     TGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTCAAAAG                         TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
genomic: TGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtg ... tcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
EST: gi|17519189|gb|BM188231.1|BM188231
EST:     TTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAG                         TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
genomic: TTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtg ... tcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
EST: gi|14991554|gb|BI317227.1|BI317227
EST:     GAAAATGTCTCTAAAAAG                         TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
genomic: GAAAATGTCTCTAAAAAGgtacttcgtg ... tcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
EST: gi|31309981|gb|CD395184.1|CD395184
EST:     TCTCTAAAAAG                         TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
genomic: TCTCTAAAAAGgtacttcgtg ... tcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
EST: gi|31458682|gb|CD400710.1|CD400710
EST:     CAGTTATGAAAATGTCTCTAAAAAG                         TGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT
genomic: CAGTTATGAAAATGTCTCTAAAAAGgtacttcgtg ... tcattttcagTGGATTCCGGAGTTGAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGTCTCTAAAAAGgtacttcgtggcaatttattgtggtcatagtgttttgggtgtatttcttcttatttattttgataattataaggtttctgtatggcctgtaatgaaggatgtatggatcatgttatatgttaagaaaataattcatttataaaaaaagtcgatgataaattgcatgtgtggtttcattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG