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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattctaaagttttctttatcttctatatttaactctgtcagctctggtgatttctgaaacagtgacaatgtggtaaatttgtattggtaaaatttattttaattttcatggtgtatttacag

Basic information

species Glycine max
transcript GLYMA01G43540.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43540.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G23920.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgta----ttattctaaagttttctttatcttctatatttaactctgtcagct-ctggtgatttctgaaacagtgacaatgtggtaaatttgtattggtaaaatttattttaattttcatggtgtatttacag
||| | ||||||||||||||  | |||||||||||||| ||||| |||||  ||| ||| |||||||| |  || ||  |||    ||||  ||||  | | |     |||||   | | |  | |  ||   |||| |    | | ||        | |||| |                                              
GTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCAgtaaggattatcttaaaactctttgatgtttctactctcatcattattcgccattggtcaggcttaatact----tgttatggtcag---------------------------------------------

upper sequence: GLYMA01G43540.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G10960.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattctaaagttttctttatcttctatatttaactctgtcagctctggtgatttctgaaacagtgacaatgtggtaaatttgtattggtaaaatttattttaattttcatggtgtatttacag
||||| ||||||||||||||| |||||||||| ||||| ||||| || ||  | | ||| ||||| ||    || || ||||| ||| | |  ||   ||  | |    ||| ||   |  |||  |||   |  |  |  |||  ||    |||| |   ||| ||||                                     
GTTCGAGATTACATTCATGTTATTGATTTAGCTGATGGACACATAGCGGCTCTACGTAAGCTAGAAGATTGCAAGATCGgtat-attatgat-ttccattcgtttctcttatctactacaatca-ttctcaagtctctt--aactttgtttgtgtgtt--gtttatattcag----------------------------------

upper sequence: GLYMA01G43540.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 5'ss of exon 6
GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgt-attattctaaagtt-ttctttatcttctat-------atttaactctgtcagctctggtgatttctgaaacagtgacaatgtggtaaatttgtattggtaaaatttattttaattttcatggtgtatttacag
|| || |||||||| |||||||||||||| ||||||||||||||||| || |||   || |||    |  |  | |||||| | |||||| || || |||||| ||    ||       || | |   | |||  | || |  | | |||     |  |||| || |||||   |     |                                  
GTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGgtcagtattctgaaattgttctttgtccatgattggtttcatgtgaaaatatcaaatttgct--tctttgatttgcttccaatttgctaaatggttgcatat----------------------------------

upper sequence: GLYMA01G43540.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 5'ss of exon 6
GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgt-attattctaaagttttctttatcttctatatttaactctgtcagctctggtgatttctgaaacagtgacaatgtggtaaatttgtattggtaaaatttattttaattttcatggtgtatttacag
|| |||||||||||||||||||| ||||||||||||||||||||||| || ||||  || |||    |  |  | |||||| | | || | || ||       || | | | | | | || ||| ||| |    ||| || ||  | ||   || |  ||  | |    |   |||| | |    || | |                
GTACGGGATTACATTCATGTTGTGGATTTAGCAGATGGGCACATTGCAGCCTTGCACAAGCTACTCAACTCAGAAATAGgttagtgttttgaaatt------gtcctttgtttatga-tccgtctgctttca-aattgctaaatgactg--gatatattagttatactatcccaaaaatgac--caagtgt----------------

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|12490049|gb|BG043570.1|BG043570
EST:     ACCATATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG                         GTTGTGAGGTCTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGA
genomic: AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGA
EST: gi|192299883|gb|FG990091.1|FG990091
EST:     AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG                         GTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
EST: gi|163918103|gb|EH039061.1|EH039061
EST:     TGCTGCATTGCTT-AACTAGATGAACCTAATATAG                         GTTGTGAGGTTTATAACCTCGTTACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: TGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
EST: gi|22933171|gb|BU550310.1|BU550310
EST:     AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG                         GTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTNNNGAGA
genomic: AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
EST: gi|9898582|gb|BE607550.1|BE607550
EST:     AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG                         GTTGTGAGGTTTATAACCTGNGAACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
EST: gi|193517169|gb|FK473409.1|FK473409
EST:     AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG                         GTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
EST: gi|57574123|gb|CX547098.1|CX547098
EST:     AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG                         GTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
EST: gi|209720496|gb|BW674679.1|BW674679
EST:     AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG                         GTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
EST: gi|57574248|gb|CX547223.1|CX547223
EST:     AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG                         GTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA
genomic: AGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattct ... gtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGgtattattctaaagttttctttatcttctatatttaactctgtcagctctggtgatttctgaaacagtgacaatgtggtaaatttgtattggtaaaatttattttaattttcatggtgtatttacag

- - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - TGCTGC