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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctttctgacaacacttgcccttgttcattgttcactaacatctctttccaccag

Basic information

species Glycine max
transcript GLYMA03G40680.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G024315_T01 (Zea mays), 5'ss of exon 5
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggac--ttaaacctttctttctgacaacac--ttgcccttgttcattgttcactaa-catctctt----tccaccag---------------------------------------------
 ||| | || |||||||| ||||||||||| || ||||||||||| ||||||||||| |  |  ||   ||||    |  ||||  |   |  ||||||||  |   || |  |  |||  || | || |   || |  |  ||  |||   |  || ||| ||||    | || ||                                              
AGAATTGGGCATTGGAATTGTACCATACAGTCCTCTTGGCCGTGGGTTTTTTGGTGGAAGAGGAGTGAAAGAACAAGTGTCTGCTGAATCTAATCTGgtatcaagtattgacacagtctacctcagaatatcatttctttcttttgttgcaaaaaaaacatttcttggtctgcatcaaaatctttttcttagttcacttacagattttactttggcttgtcag

upper sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgt--atggacttaaacctttctttctgacaacacttgcccttgttcattgttc-actaacatctctttccaccag--------------------------
||| ||||| ||||||||||| ||||| ||||| ||||||||||| || |||| ||||| ||| |  |||||| || | ||  || | ||| |  ||||  ||| | || |  || || |  | |             |||| ||||||  ||||   | | | |      |                          
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataattttctacagtaatgtt-attgttagactatgttgtgtatgtgtgtgtggaacatggtttttaaaacggtatg

upper sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0030g01990.t01 (Vitis vinifera), 5'ss of exon 5
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctt-tctgacaacacttgcccttgttcattgttcactaacatctctttccaccag---------------------------------
||||||||||||||| ||||| |||||||| || || ||||| || |||||||||||||||||||  |  |||| | | ||||||||||||||||||||||||  |  ||  | | |   ||    |   |    | |   | || |   || ||||   |   |||                                    
GGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTCGGCCGCGGGTTTTTTGGTGGCAAGGCTGCAGGGGAAAATTTGCCTGCAAACAGTTTTCTGgtatgggatggaatatgtttggcctagtgattttgataccttccccttttcttcttacatgaataatcacagtgatctaacgagaaaccttttgttttatcatcag

upper sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0030g02020.t01 (Vitis vinifera), 5'ss of exon 5
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctttctgacaacacttgcccttgttcattgttc-actaacatctctttccaccag----------------------------------------------------------------------------------------------
 |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||||||||||| ||| |  |||| |   |||||||||| ||| ||||| |||| |   |||| |  |||   |      ||  ||  ||  |||||| |||||  | |||   ||  |                                                                                               
AGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatctgacctat--ttccagccttttgtgtactcattttttgttccactaaactttctagtcaaaaacattattatggacctggatgattttgatatattcacctttgtcttacatatgaataagcatggcgaactgatgaccaaccttttgtcttatcag

upper sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0030g02050.t01 (Vitis vinifera), 5'ss of exon 5
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctttctgacaacacttgcccttgttcattgttcactaacatctctttccaccag------------------------------------------------------------------------------------------
||||||||| ||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||||||    |||| | | |||||||||||||| |||||||| |      ||  | | |         | | | ||| |  |||  | | |      || |      ||                                                                                          
GGAACTTGGGATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGCTGTTAGTGAAAATGTGCCTGCAAACAGTTTGCTGgtatgaatgcggtccaatttctggccttttgcatactcttttggattccttaatttttagtcatcatggtagttatgatccaggtgcattttgatatagtccctctttttctatgtgaattaaccatggcaaattaatggctgacctcttgtttgttatcag

upper sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0030g01980.t01 (Vitis vinifera), 5'ss of exon 5
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctttctgacaacacttgcccttgttcattgttc-actaacatctctttccaccag----------------------------------------------------------------------------------------------
 |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||| ||||||| ||| |  |||| |   |||||||||| ||| ||||| |||| |   |||| |  |||   |      ||  ||  ||  |||||| |||||  | |||   ||  |                                                                                               
AGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGCGGCAAGGTTGTTGATGAAAATGCGCCTGCAAACACTTTCCTGgtgtggaatctgacctat--ttccagccttttgtgtactcattttttgttccactaaactttctagtcaaaaacattattatggacctggatgattttgatatattcacctttgtcttacatatgaataagcatggcgaactgatgaccaaccttttgtcttatcag

upper sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0030g01970.t01 (Vitis vinifera), 5'ss of exon 5
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctttctgacaacacttgcccttgttcattgttcactaacatctctttccaccag---------------------------------------------------------------------------------------------
 |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||||||||||||||| |  |||| | | |||||||||||||| ||||| ||||   | |||| | |             | | ||| ||  |||  ||||||  | ||  || |  |                                                                                              
AGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTTGGACGTGGGTTTTTTGGTGGCAAGGCTGTTGATGAAAATGTTCCTGCAAACAGTTTCCTGgtgtggaaccagacctatttccagtcttttgtgtactcttttttgttg--cactaatttttccgtcaaaaacattattatgggcctggttggttttgatagatttccctttgtgctacatctgaataagcatggtgaactgatggccaaccttttgtcttatcag

upper sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0030g02060.t01 (Vitis vinifera), 5'ss of exon 5
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctt-tctgacaacacttgcccttgttcattgttcactaacatctctttccaccag---------------------------------
||||||||||||||| ||||| |||||||| || || ||||| || |||||||||||||||||||  |  |||| | | ||||||||||||||||||||||||  |  ||  | | |   ||    |   |    | |   | || |   || ||||   |   |||                                    
GGAACTTGGAATTGGGATAGTTCCATACAGTCCTCTCGGCCGCGGGTTTTTTGGTGGCAAGGCTGCAGGGGAAAATTTGCCTGCAAACAGTTTTCTGgtatgggatggaatatgtttggcctagtgattttgataccttccccttttcttcttacatgaataatcacggtgatctaacgagaaaccttttgttttatcatcag

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|192298310|gb|FG992100.1|FG992100
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATTTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|151410675|gb|EV280490.1|EV280490
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAAGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|14125225|gb|BG789655.1|BG789655
EST:     TTTTTGGTGGCAAGGCTGTCGTAAAAAGTATACCTGCCAACAGTTTTCTG                         GCATTTCAACCAAAGTTACCAGGGGAGAACCTTGACAAGAAC
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAAC
EST: gi|209699281|gb|BW670243.1|BW670243
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|38192802|gb|CF922008.1|CF922008
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACNTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|17998790|gb|BI245414.1|BI245414
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|21887306|gb|BQ740519.1|BQ740519
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|192332296|gb|FK025961.1|FK025961
EST:     AAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: AAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|261497124|gb|GT185192.1|GT185192
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|5761333|gb|AI966692.1|AI966692
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTCTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|58017212|gb|CX703954.1|CX703954
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|209701736|gb|BW667401.1|BW667401
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|9902294|gb|BE611262.1|BE611262
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|58014894|gb|CX701636.1|CX701636
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|213603469|gb|DB966620.1|DB966620
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|192314626|gb|FK006384.1|FK006384
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCA-CCGAG-TTGCGAGGGGAGA-CTTTGACA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACA
EST: gi|21887893|gb|BQ741106.1|BQ741106
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|254315362|gb|GR825171.1|GR825171
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAA-CAGTTT-CTG                         GCATTTCA-CCAAGGTTACGAGGG-AGA-CTTTGACA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACA
EST: gi|31464493|gb|CD406521.1|CD406521
EST:     CGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: CGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|7285866|gb|AW598353.1|AW598353
EST:     TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
EST: gi|209699282|gb|BW670244.1|BW670244
EST:     TAGAAAGTATACCTGCAAACAGTTTTCTG                         GCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA
genomic: TAGAAAGTATACCTGCAAACAGTTTTCTGgtatggactt ... tttccaccagGCATTTCAACCAAGGTTACGAGGGGAGAACTTTGACAAGAACAAAATCTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgtatggacttaaacctttctttctgacaacacttgcccttgttcattgttcactaacatctctttccaccag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG