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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGGAGGGAAGATCAGCCTGGGCTGCTTTTTGGGTTATTTTAGTTGGCTTAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttgtcacattttcagtttggtgatgctattagatatttagatgcctttttttattcaattctaaattttatatagcattgtggcatgcaacgagaagcattaaattcggtatcatctgagacttgttagaaactcaaatatgagaacatgaaatttgcaatttaccggtatttttgttggtgtttttgcag

Basic information

species Glycine max
transcript GLYMA20G27000.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G27000.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 11
TCAGGAGGGAAGATCAGCCTGGGCTGCTTTTTGGGTTATTTTAGTTGGCTTAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttgtcacattttcagtttggtgatgctattagatatttagatgcctttttttattcaattctaaattttatatagcattgtggcatgcaacgagaagcattaaattcggtatcatctgagacttgttagaaactcaaatatgagaacatgaaatttgcaatttaccggtatttttgttggtgtttttgcag
                                          |||||     |||||||| || | | |    ||  ||||||||||||||||| ||||||||||||    |||||   ||   |     | || || | | ||| | ||  | |   | ||  ||  | | |  | |      |   ||| |    |        |||  |   | |  |||||    ||||||                                                               
------------------------------------------AGTTGTTGCTGTTGTGGCAGCGGGAAGT---TATGTTGTGTACAAATACAGACTAAGGGTAAGCT--AGCACATGCACACCCT-----TACTTTT-GTTCTTTCGTTGTTTgtccatgtttcatgatgagtgattttctatctctgggcctattcc--------ttatgt--aggaatatctgttttttgtta---------------------------------------------------------------

upper sequence: GLYMA20G27000.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G303631_T03 (Zea mays), 5'ss of exon 11
TCAGGAGGGAAGATCAGCCTGGGCTGCTTTTTGGGTTATTTTAGTTGGCTTAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttgtcacattttcagtttggtgatgctattagatatttagatgcctttttttattcaattctaaatt-ttatatagcattgtggc-atgcaacgagaagcattaaattcggtatcatctgagacttgttagaaactcaaatatgagaacatgaaatttgcaatttaccggtatttttgttggtgtttttgcag
     |||  | | |||| ||||||||  | |||| ||| ||  | |   | | ||| |  || || ||    ||  ||||||||||||||||| ||||||||||||    |||||   ||   |     | || || | | ||| | ||  | |   | ||  ||  | | |  || | || |  || | | || |     | || |                                                                                            
AGTTCAGGCTAAAGCAGCATGGGCTGCAGTGTGGGGTATCTTGATAGTTGTTGCTGTTGTGGCAGCGGGAAGTTATGTTGTGTACAAATACAGACTAAGGgtaagct--agcacatgcacaccct-----tactttt-gttctttcgttgtttgtccatgtttcatgatgagtgattttctatctctgggcctattccttatgtagga--------------------------------------------------------------------------------------------

upper sequence: GLYMA20G27000.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 5'ss of exon 11
-TCAGGAGGGAAGATCAGCCTGGGCTGCTTTTTGGGTTATTTTAGTTGGCTTAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttgtcacattttcagtttggtgatgctattagatatttagatgcctttttttattcaattctaaattttatatagcattgtggcatgcaacgagaagcattaaattcggtatcatctgagacttgttagaaactcaaatatgagaacatgaaatttgcaatttaccggtatttttgttggtgtttttgcag
  | | || ||| ||| || ||||||||  | ||||| |||||  ||||||| | | |||||| | | || ||||| |||||||||||||| ||||||||||||||||| ||               |  || || ||   | |   ||      | |   | ||    |  |   | || |   | |  ||  |||  |     ||     |  |                                                                                   
AACTGAAGTGAA-ATCTGCATGGGCTGCAGTCTGGGTAATTTTGATTGGCTTGGCTATGGCTGGTACTGGAGCATATCTTGTGTACAAATATAGAATAAGGgtaagcttggt---------------gcaatacttttctgtgtgctgactttactctgactgcagcattggagcctttagactgtaggtgctagcattggccttcaccctttctg-----------------------------------------------------------------------------------

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|151401547|gb|EV271361.1|EV271361
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|193608690|gb|FK562408.1|FK562408
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATATAGAATAAGG                         TCATATATGGATTCT
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCT
EST: gi|6482170|gb|AW201441.1|AW201441
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAAAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|193403963|gb|FK367333.1|FK367333
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|208198729|gb|GD998494.1|GD998494
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|31463161|gb|CD405189.1|CD405189
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|193650422|gb|FK595797.1|FK595797
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|21601067|gb|BQ611398.1|BQ611398
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|13312023|gb|BG405674.1|BG405674
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|193619425|gb|FK571293.1|FK571293
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
EST: gi|298197470|gb|HO044949.1|HO044949
EST:     TAGTTGTGGCTGCTGCAGGGGCATACCGTGTGTACAAATACAGAATAAGG                         TCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG
genomic: TAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttg ... gtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGGAGGGAAGATCAGCCTGGGCTGCTTTTTGGGTTATTTTAGTTGGCTTAGTTGTGGCTGCTGCAGGGGCATACCTTGTGTACAAATACAGAATAAGGgtaagctttgtcacattttcagtttggtgatgctattagatatttagatgcctttttttattcaattctaaattttatatagcattgtggcatgcaacgagaagcattaaattcggtatcatctgagacttgttagaaactcaaatatgagaacatgaaatttgcaatttaccggtatttttgttggtgtttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG