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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGGTAATAGCTTTACATATAATAGCAGCATCAATATTGCAGTTGCTGTGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaatactctagtttaagcagcttctagtccccccatctcccacttttctaatataagatggttctttattgtaaaatggtatatttgatgtatattgtag

Basic information

species Glycine max
transcript GLYMA20G31630.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31630.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G165176_T01 (Zea mays), 5'ss of exon 4
AGATGGTAATAGCTTTACATATAATAGCAGCATCAATATTGCAGTTGCTGTGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaatactctagtttaagcagcttctagtccccccatctcccacttttctaatataagatggttctttattgtaaaatggtatatttgatgtatattgtag
 ||||| || ||||| || || |  || || ||||| ||||| || || ||||| |||||||||||  ||||||||||||| ||||| | ||||||||||||   | || ||| ||   |   ||     |  |       |     | |||| | | |||| ||||||  ||  ||    |||                      
GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgt---caaacactttaccatgcacaatgagtgttgatatttttgatgattttttttaaataa-atggttacttgctggtttatgcag-------------------

upper sequence: GLYMA20G31630.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G036534_T02 (Zea mays), 5'ss of exon 3
AGATGGTAATAGCTTTACATATAATAGCAGCATCAATATTGCAGTTGCTGTGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaatactctagtttaagcagcttctagtccccccatctcccacttttctaatataagatggttctttattgtaaaatggtatatttgatgtatattgtag
 ||||| || ||||| ||||| || |  || || || ||||| || || ||||| |||||||||||  |||||||||| || ||||| | ||||||||||||   | || ||| ||   |   |      |  |         |     ||||  || |||| ||||||   |  ||    |||                      
GGATGGAAAGAGCTTCACATACAACAAAAGTATAAACATTGCTGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCGGTTCTTCAAGATGCTGATAAGgt---caaacactttaccatgcacgatgaatgctgatttttgataattttttttaaaaataa-atggttacctggtggtttatgcag-------------------

upper sequence: GLYMA20G31630.1 (Glycine max), 5'ss of exon 3
lower sequence: AT1G34430.1 (Arabidopsis thaliana), 5'ss of exon 2
AGATGGTAATAGCTTTACATATAATAGCAGCATCAATATTGCAGTTGCTGTGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaatactctag----tttaagcagcttctagtcc-ccccatctcccacttttctaatataagatggttctttattgta-aaatggtatatttgatgtatattgtag
||||||||| || |||   |||||||| ||||||||  |||| |||||||| ||||| ||||||||  |||| || || |||||||||   |||||||||||| |    |  | ||     | ||||    ||  |||   | |  | | | |      ||  |   | | ||||| | || |  |||  |                     
AGATGGTAACAGTTTTGTGTATAATAGTAGCATCAACGTTGCTGTTGCTGTTGCTATTGATGGTGGTTTGATCACTCCGGTGCTTCAGAACGCTGATAAGgttcttttcttttgtatgctttataagagattttgagtttactctgtattcaaaaccggtatcagtgggttgttctatcttttgtaaacag---------------------

upper sequence: GLYMA20G31630.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 5'ss of exon 2
AGATGGTAATAGCTTTACATATAATAGCAGCATCAATATTGCAGTTGCTGTGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat--actctagtttaagcagcttctagtccccccatctcccacttttctaatataagatggttctttattgtaaaatggtatatttgatgtatattgtag
||||||||| |||||||||||||| || || ||||||||||| ||||| ||||| |||||||||||  ||||||||||||||||||||| ||||||||||||||   |||    ||| | | ||     || | |   ||| ||      |||||| |   | | ||      | |||| ||  |  ||||                 
AGATGGTAAGAGCTTTACATATAACAGTAGTATCAATATTGCGGTTGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTGCTTCAGGATGCTGATAAGgtttgttaatctgttcttgctaaacttaattttggctaccctatg----gcttttcaagagttaaat------taattgcaatttattatag----------------

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|5760606|gb|AI965969.1|AI965969
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGATTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|208192888|gb|GD987937.1|GD987937
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|208334221|gb|GE130038.1|GE130038
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|192313139|gb|FK003721.1|FK003721
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|193375685|gb|FK340482.1|FK340482
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|18039518|gb|BM307812.1|BM307812
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|207833145|gb|GD805294.1|GD805294
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|7691381|gb|AW759439.1|AW759439
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|208249676|gb|GE045439.1|GE045439
EST:     ACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: ACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|208158340|gb|GD956889.1|GD956889
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|208285478|gb|GE083436.1|GE083436
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGG
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGG
EST: gi|208031676|gb|GD831212.1|GD831212
EST:     GGCTATAGATGGTGGACTGTATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: GGCTATAGATGGTGGACTG-ATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|298180893|gb|HO022332.1|HO022332
EST:     GGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: GGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|193364815|gb|FK330524.1|FK330524
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGG
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGG
EST: gi|192313138|gb|FK003720.1|FK003720
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|7591481|gb|AW707213.1|AW707213
EST:     TGGCTATAGATGGCGGATTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|193523358|gb|FK482713.1|FK482713
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
EST: gi|208036483|gb|GD834832.1|GD834832
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAG
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAG
EST: gi|193376952|gb|FK340587.1|FK340587
EST:     TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAG                         ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC
genomic: TGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaat ... tatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGGTAATAGCTTTACATATAATAGCAGCATCAATATTGCAGTTGCTGTGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaatactctagtttaagcagcttctagtccccccatctcccacttttctaatataagatggttctttattgtaaaatggtatatttgatgtatattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT