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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctcattttatagattacatgcatttctttcaacctttttttcctagttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag

Basic information

species Glycine max
transcript GLYMA17G34690.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os01g51410.2 (Oryza sativa), 5'ss of exon 9
AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctcattttatagattacatgcatttctttcaacctttttttccta-gttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag
||| || ||||| ||||||||||||||||||||||| || ||||| ||||| |||||||| || || ||||||||||||||||||||||| ||  ||||||| | | |  |  |   ||| || | |     || | ||||  |||   |  ||| | |   || |  | | | | |    ||| | |||| |  |                
AATTTCCTACACATACATAGCCATGATGGGTTCTAAGGGTCTCACTGATGCTTCAAAGATTGCAATCTTGAATGCAAACTACATGGCAAAGCGTCTGGAGgtatatttgttactcgtgatcacttac--ccattgctacctagtttgattgtgtttgaac--tagttttctaagttttaccatgttacttg-tacag---------------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os06g40940.3 (Oryza sativa), 5'ss of exon 9
AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctcattttatagattacatgcatttctttcaacctttttttcctagttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag
||| || ||||| ||||||||||||||||||||||| || ||||| ||||| |||||||| || || |||||||||||||||||| |||| ||  ||||||| | | |  |  |   ||| || |  ||| ||  | |  ||  ||     ||| | |  |   | ||  | ||    || | | |  |                      
AATTTCCTACACATACATAGCCATGATGGGTTCTAAGGGTCTCACTGATGCTTCAAAGATTGCAATCTTGAATGCAAACTACATGACAAAGCGTCTGGAGgtatatttgttactcgtgatcacct--attgctacctagtttgattgt---gtttgaactagttttctaagttttaccatgttacctgtacag------------------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G104310_T02 (Zea mays), 5'ss of exon 8
AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctcattttatagattacatgcatttctttcaaccttt---ttttcctagttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag
||| || ||||| || |||||||||||||| ||  | || ||||| ||||| || ||||| || || ||||||||||||||||||||||||||  | |||||      ||||||   ||   ||| | ||     ||    ||   ||  || | ||||| |  ||| |||   | |  ||| ||| || |   |  |                
AATTTCCTACACATATATAGCCATGATGGGCTCACAGGGGCTCACTGATGCTTCGAAGATCGCGATCTTGAATGCAAACTACATGGCAAAACGTCTAGAGgt--actacattttcacgacagcataccttggcggcatttgttacattcgccaaattagtcttctaaaactt--acttggta-atggtcttct-tgcag---------------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G098568_T01 (Zea mays), 5'ss of exon 3
------------AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctcattttatagattacatgcatttctttcaaccttt---ttttcctagttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag
            ||| || |||||  | ||||||||||||||          ||||| ||||| |||||||| || || ||||||||||||||||||||||||||  | |||||    |   ||    | | ||||| |  |  || ||    ||   ||   | | ||||| |  ||| | |   | |  ||| |||||| |   |  |                
TTTGATTATGCCAATTTCCTACAC--ATATAGCCATGATGGG----------CTCACTGATGCTTCAAAGATTGCGATCTTGAATGCAAACTACATGGCAAAACGTCTAGAGgtactaccttttcatgacaatacataccatagttgcatttgttacattcatcaaattagttttctaaaattt--acttggta-atgatcttct-tgcag---------------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 10
lower sequence: AT4G33010.1 (Arabidopsis thaliana), 5'ss of exon 9
AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctcattttatagattacatgcat-ttctttcaacctttttttcctagttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag
 || ||||| |||||||| ||||||||||| |||   || ||||| ||||| || ||||| || ||||||||||| || ||||||||||| ||  | |||||             ||||  |  |   | |||| |  |||| ||  || |  | || || | |  | | | ||| |     ||||  ||| ||| ||              
TATATCTTATACTTACATTGCCATGATGGGATCTGGTGGGCTCACTGATGCCTCTAAGATTGCAATTTTGAATGCCAATTACATGGCAAAGCGCCTAGAGgta-----------gtagaacatctttgtcttctatttacctattcatcttt-tgagaatgaaaggagtctaattttcctcttgat--ttgtttttacag------------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 10
lower sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 10
AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgt---ttgtctcattttatagattacatgcatttctttcaacctttttttcctagttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag
|||||| || |||||||| ||||||||||| |||  ||||||||||||||| |||||||| || |||||||| || |||||||||||||| ||  |||||||   || ||| || ||    | |   |  |     |  |    | || || |    |   |||   |  ||   |  ||| | | |                           
AATCTCGTATACTTACATTGCCATGATGGGATCTGGAGGACTCACCGATGCCTCAAAGATTGCAATTTTGAACGCTAACTACATGGCAAAGCGTCTGGAGgtaccttatcttatcttgacaactctttaaagagagtgaacgtctcttctcttgtgcaacctcac--ttatgctttcttgtctttcag--------------------------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 5'ss of exon 11
AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctcattttatagattacatgcatttctttcaacctttttttcctagttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag
 || || ||||| ||||| ||||||||||| ||||| |||||||| || || |||||||| || ||  |||| |||||||||||||| ||||| ||||||||          || | ||| |        || ||   |   || ||  | |   | |   | | | | |||    | || || | |  | | ||   |   || ||| | 
GATTTCATACACCTACATTGCCATGATGGGGTCTAAGGGACTCACTGAAGCCTCAAAGATTGCGATCCTGAAAGCAAACTACATGGCCAAACGCTTGGAGgtccacaaatcattcttgatca--------tccttttgctaattatt--tggaccgcacgttcaaattttgaacagggatttg-ttcaagatctaggatcaccttctaaaa

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 5'ss of exon 10
AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgt-ctcattttatagattacatgcatttctttcaacctttttttcctagttagtatcataa-tactgtgattctgtatat--gatccttggtttaac--tttgactcctacag-----------------------
||| || || ||||||||||| |||||||| ||||| |||||||| ||||||||||||||||| ||| | ||||||||||||||||||||||| ||||||||   | ||  ||   |  ||  | | | ||  ||| | |  ||  |    | | ||     ||   |  | || |    ||    |||  ||  | ||||  ||| | |      |                       
AATATCATATACTTACATAGCAATGATGGGATCTAAGGGACTCACTGATGCATCAAAGATAGCTATTCTCAATGCAAACTACATGGCAAAACGTTTGGAGgtccctgcttcttccttgaatatcttcccttggttttatcagttaataagaaatcagggcagtaggcatagggacttgaaattctagattatttttgtaaccttttcattgtgtttgtgtttttgctttgcgttcctcag

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|20448765|gb|BQ252889.1|BQ252889
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|16276767|gb|BI942033.1|BI942033
EST:     CATCAAAGATAGCCATCTTGATTGCAAACTACATGCCAAAACGATCGGAG                         AATTAT-ATCCCGTTCTTTTCCGTGGAGTCA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCA
EST: gi|26058323|gb|CA801237.1|CA801237
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|154204736|gb|EV554998.1|EV554998
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|209717715|gb|BW671533.1|BW671533
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|20075344|gb|BQ094127.1|BQ094127
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTA-CCCGGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCG-TTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGA
EST: gi|120493515|gb|EH221682.1|EH221682
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|10231306|gb|BE800194.1|BE800194
EST:     AAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: AAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|192295731|gb|FG990825.1|FG990825
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|13480387|gb|BG509730.1|BG509730
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|20812005|gb|BQ296483.1|BQ296483
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTA-CCCGGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCG-TTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGA
EST: gi|16281624|gb|BI944583.1|BI944583
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGT-AATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|192315105|gb|FK009929.1|FK009929
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|192315106|gb|FK009930.1|FK009930
EST:     AAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: AAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|15589745|gb|BI674361.1|BI674361
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|117557747|gb|EG702132.1|EG702132
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
EST: gi|154204730|gb|EV554992.1|EV554992
EST:     CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAG                         AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA
genomic: CATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctca ... actcctacagAATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCTCTTACACTTACATAGCCATGATGGGTTCTAAAGGACTCACCGATGCATCAAAGATAGCCATTTTGAATGCAAACTACATGGCAAAACGATTGGAGgtttgtctcattttatagattacatgcatttctttcaacctttttttcctagttagtatcataatactgtgattctgtatatgatccttggtttaactttgactcctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG