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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtgaatgtggcttttgcagaagcaactattttgcatgagcctcttttttcttgtcttgatgccttgtttaccagtattctttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG

Basic information

species Glycine max
transcript GLYMA15G04500.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
tttgtgaatgtggcttttgcagaagcaactattttg-catgagcctcttttttct-tgtcttgatgccttgtttaccagtattctttcattcttgata-atagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG-------------
    | | |     |  ||  | | |||||||  |  ||  |  | || |  ||  |||  || |      || |    | ||   | ||| |  | | | |||| || ||||| |||||||| || |||||||||||||||||||| || ||  | ||||| | ||||||| |||| ||||| |||||              
acattcattacccgtggtgatgcaacaactatactaacacaaatcactatgatccatgtagtggtagaa-attgatt--tgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG

upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
tttgtgaatgtggcttttgcagaagcaactattttgcatgagcct--cttttttcttgtcttgatgccttgtttaccagtattctttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG
  | || || ||| | |    ||   |  |  | |     ||     || | |||||     ||||  |    |    |  || |||  ||     |   |||| || ||||| || ||| |  | |||||||||||||||||||| |||||| | ||||| |   |||||||||| ||||| ||||||
--tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG

upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
------tttgtgaatgtggcttttgcagaagcaactattttgcatgagcctcttttttcttgtcttgatgccttgtttaccagtattctttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG
      |  |    || || |||   ||    | || || ||  | |       || | |  |  |      ||  ||     | |||||   |  ||  |  ||| |||| ||||| |||||| |  ||||||||||||| |||||||| |||||||| ||||| |   | ||||||||||| || ||||||
acagaatcagatcttggggttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttactt-----ttttcttgtttgttttgtg-tagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG

upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
tttgtgaatgtggcttttgcagaagca-actattttgcatgagcctcttttttcttgtcttgatgccttgtttaccagtattc-tttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG
  |   |   |  | ||      | || |  |||   |  || | |   |||| || |||| |     |   |||    |||| ||||| |||||||   ||||||| |||||||| ||||| ||||||||||||||||||||||| || || || || ||||   |||||||||||||||| ||||||
--tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG

upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------tttgtgaa-tgtggcttttgc----agaagcaactattttgcatgagcctcttttttcttgtcttgatgccttgtttaccagtattctt----tcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG
                                                                                 | || || |||   |  | |    ||    ||||  |||    ||   | |   |  | ||      | |||||| |     ||  ||    |  || |   |   || | || ||||| |||||| | || ||||||||||||||||| ||||||||||| || |||||  | |||||| | |  | ||| || 
gtaagcacgcaaatcaattcttggccagacctaattggtggaagttatgtagtccaggtttaaaacggtggttgtgattcatcgtaaactgttattactacctccagctttaactgcttttttagaagttgtgcatcgtcgtgactcagtcttgttgatttaaatatttgaggtatttttccgtttcagGCGAAGATGAGGATCTTGATCACAGGAGGAGCTGGATTCATCGGGTCTCACTTGGTCGACAGGCTCATGGAAGAGGGCACAAACGAA

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|213611728|gb|DB962965.1|DB962965
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|8827206|gb|BE210936.1|BE210936
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|151412093|gb|EV281905.1|EV281905
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|192316740|gb|FK006443.1|FK006443
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|213591579|gb|DB955787.1|DB955787
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|10237388|gb|BE806276.1|BE806276
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|213592188|gb|DB965979.1|DB965979
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|192316741|gb|FK006444.1|FK006444
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|16279667|gb|BI943554.1|BI943554
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|192317198|gb|FK007909.1|FK007909
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TTCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
EST: gi|192296657|gb|FG991225.1|FG991225
EST:     CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAG                         TCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC
genomic: CAAAGCAGCCTCCTTTGCCATCTCCCCTGCGCTTTTCCAAATTTTTTCAGgtgaagcatt ... ttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttcttgtcttgatgccttgtttaccagtattctttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG
                                           tcttgat  putative branch site (score: 4)
                                tattctttcattctt  CT-rich tract
                                             ttgataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtgaatgtggcttttgcagaagcaactattttgcatgagcctcttttttcttgtcttgatgccttgtttaccagtattctttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA