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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCCATCTCCTTTATCGGAATAAGAAGGTAGATTTTATTGAACAGTTCAATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaattttctcctttacgtgcattgtgtatacatgattctacatccagtcatctgacttgtaattaattttag

Basic information

species Glycine max
transcript GLYMA04G40290.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40290.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os05g40410.1 (Oryza sativa), 5'ss of exon 6
CAGCCATCTCCTTTATCGGAATAAGAAGGTAGATTTTATTGAACAGTTCAATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaattttctcctttacgtgcattgt-gtatacatgattctacatccagtcatctgacttgtaattaattttag---------------
|| ||| |||||  |||||||||||||||| ||||| ||||||||||||||||||||||| || || ||||| |||   |||||||| || || |||||||||| |  ||| | |   | |    |||||  | ||||         | | | | |  |   ||||      |||||                
CAACCACCTCCTCCATCGGAATAAGAAGGTTGATTTCATTGAACAGTTCAATGAAAAGCTCCTGGTCAAGCAGGAAGGAGAGAATCTTCAAATACTTGATgtaatt--tttcccctaatgccacaattgtcatttacaatcaagagaaacaaattacttttattgtttaggtttttaacactcggtattgtag

upper sequence: GLYMA04G40290.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G145662_T01 (Zea mays), 5'ss of exon 6
CAGCCATCTCCTTTATCGGAATAAGAAGGTAGATTTTATTGAACAGTTCAATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaattt-tctcctttacgtgcattgtgtatacatgattctacatccagtcatctgacttgtaattaattttag--------------
|||||| |||||  |||| || |||||||||||||||||||| ||||||||||||||||| || || ||||| |||   ||||| ||||| |||||||||||||| | | |  ||  || |     |    | |||  || |||   ||  ||   | | ||    || | | ||  |              
CAGCCACCTCCTCCATCGTAACAAGAAGGTAGATTTTATTGAGCAGTTCAATGAAAAGCTTCTGGTCAAGCAGGAAGGAGAGAACCTCCAAATTCTTGATgtaagcattatacctaattcaaccaaacaaagaatatttgcttcgttattaagggttttaaccctgaactcacttgtgcacctaatatctag

upper sequence: GLYMA04G40290.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G138840_T01 (Zea mays), 5'ss of exon 6
CAGCCATCTCCTTTATCGGAATAAGAAGGTAGATTTTATTGAACAGTTCAATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaattttctcctttacgtgca--ttgtgtatacatgattctacatccagtcatctgacttgtaattaattttag--------------
|||||| || ||  |||| || |||||||||||||| ||||||||||||||||||||||| || || ||||| |||   |||||||| || ||||||||||||||   |   |     | |   ||      | |||  || |||  |||  ||   | | |||   || | | ||                 
CAGCCACCTTCTCCATCGTAACAAGAAGGTAGATTTCATTGAACAGTTCAATGAAAAGCTTCTGGTCAAGCAGGAAGGGGAGAATCTTCAAATTCTTGATgtaagccttacacctaaatgcagtcaaacaaagaatatttgtttcatcatt-agcgttttaactctgaactcacttgtacctaatacctgtag

upper sequence: GLYMA04G40290.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv13s0067g00100.t01 (Vitis vinifera), 5'ss of exon 6
CAGCCATCTCCTTTATCGGAATAAGAAGGTAGATTTTATTGAACAGTTCAATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaattttctcctttacgtgcattgtgtatacatgattctacatccagtcatctgacttgtaattaattttag
|| |||||| ||| |||||||||||||||| ||||| ||||||||||||||||||||||| || || ||||||||||| |||||||||||||||||||||||||| |  ||| || ||  | || |    ||   | |   | |||||   |  ||||   |  || ||  ||  ||
CAACCATCTGCTTCATCGGAATAAGAAGGTGGATTTCATTGAACAGTTCAATGAAAAGCTTCTTGTCAAGCAAGAAAACGAGAATCTCCAGATTCTTGATgtaagaatctttgtctttgtcttgaaaca-gtgagcttttatttacatat-gaaatctagatgctatttctttgcag

upper sequence: GLYMA04G40290.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S21_398V6.1 (Physcomitrella patens), 5'ss of exon 6
CAGCCATCTCCTTTATCGGAATAAGAAGGTAGATTTTATTGAACAGTTCAATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaattttctcctttacgtgcattgtgtatacatgattctac--atccagtcatctgacttgtaattaattttag--------------------------------------------------------------------------
 |  ||||| ||| |||| || || || || || ||||||||||||||||| || || || || || |||||||||||||||||||| || ||||||||||| |||    ||       | ||  ||  |  ||   ||| ||| |  |     |      | | |  ||  ||||                                                                             
TAATCATCTTCTTCATCGAAACAAAAAAGTTGACTTTATTGAACAGTTCAACGAGAAACTGCTTGTCAAGCAAGAAAATGAGAATCTGCAAATTCTTGATgtgagtttcattgaaaacgaagtaaatc-tccatttttgaatctcctgagttgcttgaactattcgatatcgatttctttagagattgtgcgtttgatgctgtattctgtctacaatatggtcggtgctaatgtctgaaataccaatttgcag

upper sequence: GLYMA04G40290.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S34_176V6.1 (Physcomitrella patens), 5'ss of exon 6
CAGCCATCTCCTTTATCGGAATAAGAAGGTAGATTTTATTGAACAGTTCAATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaattttctcctttacgtgcattgtgtatacatgattctacatccagtca--tctgacttgtaattaattttag----------------------
||  ||||| ||  |||| || ||||| || || || || |||||||||||||||||||| || || |||||||||||||||||||| ||||||||||||||||||  |  |    |  |  |||  |    || | |  ||| |  || |   |  | |  ||  | |||||    ||                      
CAATCATCTGCTACATCGAAACAAGAAAGTTGACTTCATCGAACAGTTCAATGAAAAGCTGCTTGTCAAGCAAGAAAATGAGAATCTTCAGATTCTTGATgtaagtt-tcatacattcaaaatgctctactcatcctttgttcaatctctaaaaaactttccctctttattaagaaaagatgctgcagtctttggataggt

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|193720245|gb|FK655389.1|FK655389
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACGCCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|207686706|gb|GD670052.1|GD670052
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|193562217|gb|FK516942.1|FK516942
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|193550229|gb|FK510262.1|FK510262
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|208066904|gb|GD867207.1|GD867207
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGGT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|58018556|gb|CX705298.1|CX705298
EST:     ATGANNAGCTACTCGTAAAGCAAGACAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|193445118|gb|FK409296.1|FK409296
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|19269973|gb|BM886229.1|BM886229
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|193719371|gb|FK653495.1|FK653495
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTT-GAACACACAGAAGTTTGCAGAAGTGTAATTTATGACACC
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTG-AATTTATGACACC
EST: gi|208189266|gb|GD985644.1|GD985644
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGGT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|193410309|gb|FK380216.1|FK380216
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTA
EST: gi|193452984|gb|FK418564.1|FK418564
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|193555344|gb|FK511029.1|FK511029
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGTACTTTTGAA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGG-ACTTTTGAA
EST: gi|120529430|gb|EH257564.1|EH257564
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACA
EST: gi|207717162|gb|GD697656.1|GD697656
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
EST: gi|208175143|gb|GD970434.1|GD970434
EST:     ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGAT                         GTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA
genomic: ATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaatt ... ttaattttagGTTCGGACTTTTGAACACACAGAAGTTTGCAGAAGTGAATTTATGACACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCCATCTCCTTTATCGGAATAAGAAGGTAGATTTTATTGAACAGTTCAATGAAAAGCTACTCGTAAAGCAAGAAAATGAGAATCTCCAGATTCTTGATgtaagtaattttctcctttacgtgcattgtgtatacatgattctacatccagtcatctgacttgtaattaattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA