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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgccacttgcatagctctttgcactgtggttttcatggactcattaatacaatccttgttgcatgatttttgaatatgattatggaactgattggacttcattccag

Basic information

species Glycine max
transcript GLYMA08G08970.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G08970.2 (Glycine max), 5'ss of exon 4
lower sequence: AT2G34470.2 (Arabidopsis thaliana), 5'ss of exon 5
CAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgc-cacttgcatagctctttgcactgtggttttcatggactcattaatacaatccttgttgcatgatttttgaatatgattatggaactgattggacttcattccag
 || ||| | ||||||||||| || ||||| || || || || |  ||||||||||| || || ||||| || ||||||||||| ||||||||||| || ||  |      ||  | || |||||  |    |  |||| ||  | ||  || ||   |       | | || | |    |    || |  |||||                 
TAGAGAACTAGCTGACTATATCATCTACATCATCGATGTATCGGCTGGTGATAAAATACCCCGTAAAGGCGGCCCTGGAATCACTCAAGCTGATCTTCTGgtgcgcttatgctgccttaactcttcacttactccttttgatcaagtctatagtagtgt-------gaaagaatctcttgtggatttttccaactgcag--------------

upper sequence: GLYMA08G08970.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv10s0003g03120.t01 (Vitis vinifera), 5'ss of exon 9
CAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgccacttgcat------agctctttgcactgtggtt--ttcatggactcattaatacaatccttgttgcatgatttttgaatatgattatggaactgattggacttcattccag
|||||||||||| |||||||||||||| |||||||| || ||||| ||||| ||||||||||||||||| || || || || || |||||||||||||| ||| |||     |   |      || | |     |||  |||  ||   | |||||  || |  ||||  |    | ||  |||||   | |  | ||   |||||    |  |||  ||
CAGGGAATTGGCCGACTATATTATTTATATAATAGATGTATCTGGTGGTGACAAAATTCCTCGGAAAGGAGGCCCAGGCATAACCCAAGCTGATCTCCTAgtatgtgttttctaattctcttcagttatacctgctgcagttacttttggcactcagaaagaagatccaagcattaggaagtttgacagtaacga-gggtttgatt---ttgaattgtag

upper sequence: GLYMA08G08970.2 (Glycine max), 5'ss of exon 4
lower sequence: PP1S101_185V6.4 (Physcomitrella patens), 5'ss of exon 6
CAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgccacttgcatagctctttgcactgtggttttcatggactcattaatacaatccttgttgcatgatttttgaatatgatta--tggaactgattggacttcattccag
||||||  |||| ||||| ||||||||||| || || || || || ||||||||||||||||| || |||||||| || ||||| ||||| ||||| ||||||||    | ||| | |     || ||   ||      | | ||  |  ||     ||   | |     |   ||||| |     |  || ||     | |   |        
CAGGGAGCTGGCAGACTACATTATTTACATCATTGATGTATCCGGTGGTGATAAAATTCCTCGCAAGGGTGGTCCAGGCATCACTCAAGCAGATCTTCTTgtaagattta-ttgaaga-----ttacagaatgtagaaaaagcacgtag-aaggttgtctacgatcggcaaaagttgaaaagtgcgagttgcaatcagctagttgtt-------

upper sequence: GLYMA08G08970.2 (Glycine max), 5'ss of exon 4
lower sequence: EFJ34189 (Selaginella moellendorffii), 5'ss of exon 5
CAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagt-gccacttgcatagctctttgcactgtggttttcatggactcattaatacaatccttgttgcatgatttttgaatatgattatggaactgattggacttcattccag
||||||| | || ||||| || || || || || || || ||||| || || ||||||||||| ||||| || ||||| ||||| ||||| |||||||||||||||  |   |    | ||||  | |||| | |  |  |   |      |                                                             
CAGGGAACTAGCCGACTACATCATCTATATTATCGATGTCTCTGGGGGCGACAAAATTCCTCGCAAAGGCGGGCCTGGTATCACACAAGCCGATCTCCTTgtaagttacttttcattttgctcgctccactctcgactgaagaaaacgcacag------------------------------------------------------------

upper sequence: GLYMA08G08970.2 (Glycine max), 5'ss of exon 4
lower sequence: EFJ21803 (Selaginella moellendorffii), 5'ss of exon 5
CAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagt-gccacttgcatagctctttgcactgtggttttcatggactcattaatacaatccttgttgcatgatttttgaatatgattatggaactgattggacttcattccag
||||||| | || ||||| || || || || || || || ||||| || || ||||||||||| ||||| || ||||| ||||||||||| |||||||||||||||  |   |    | ||||  | |||| | |  |  |   |      |                                                             
CAGGGAACTAGCCGACTACATCATCTATATTATCGATGTCTCTGGGGGCGACAAAATTCCTCGCAAAGGCGGGCCTGGTATCACGCAAGCCGATCTCCTTgtaagttacttttcattttgctcgctccactctcgactgaagaaaacgcacag------------------------------------------------------------

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|193443497|gb|FK404651.1|FK404651
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|193603908|gb|FK557655.1|FK557655
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|208133691|gb|GD931764.1|GD931764
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGA
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGA
EST: gi|208107836|gb|GD902012.1|GD902012
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|193386654|gb|FK349915.1|FK349915
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCCCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|207780309|gb|GD752118.1|GD752118
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTG
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTG
EST: gi|208223074|gb|GE024781.1|GE024781
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|208160488|gb|GD960436.1|GD960436
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|193724751|gb|FK658511.1|FK658511
EST:     TAAAATTACCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: TAAAATT-CCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|207794539|gb|GD767188.1|GD767188
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|193362412|gb|FK326972.1|FK326972
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
EST: gi|9259040|gb|BE347187.1|BE347187
EST:     ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTT                         GTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC
genomic: ATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgcca ... ttcattccagGTGATAAACAAGACTGACCTTGCTCCTGCAATTGGGGCTGATTTGGCAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGAATTGGCTGACTATATTATTTACATAATAGACGTGTCTGGCGGTGATAAAATTCCTCGGAAAGGTGGTCCTGGAATCACGCAAGCTGATCTCCTTgtaagtgccacttgcatagctctttgcactgtggttttcatggactcattaatacaatccttgttgcatgatttttgaatatgattatggaactgattggacttcattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT