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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag

Basic information

species Glycine max
transcript GLYMA08G44410.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag
 || ||||   | |  |||||  | || ||    ||||| || |||||||||||||||||||| ||||||||||| ||||| || |||||| ||||||||||     |  |    ||| |   | |       |||| |     | ||||    |||  |  |   |   ||  |   | ||   |||                                     
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagct-----accatggctctgt-ttactaaacatgttgcttcaatatttttcag------------------------------------

upper sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G014313_T02 (Zea mays), 5'ss of exon 3
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatca-tgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag
|||||| |   | |  |||||  | || |||   ||||| ||||||||||||||||||||||| ||||||||||| ||||| || |||||| ||||||||||  |    |  |  |       |  ||| |   |  | | | | |   |  || |||    || | ||   | |||    |  | ||| |  ||| |  || ||  |                  
TCCAAAGGAAGACGCGCAGAAGGCTCAGGCAGCCATGTTTTCTGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTATCCATGATAGTTCCTCAGgttctgtgttccg--tacactgatttacttgtggtgcactatagttggctaatcgtgtggcattctaccgtatgttatatta-acatca-taacttgtgtttttgcag------------------

upper sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtg--ttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag
||| || ||  | |  || ||||| |||||    ||||| |||||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||||||||||  ||  | ||| | | |  ||   |  |   |||   ||   | ||||            | |  |  |  |||  |                                               
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgtatttgaaatgtttca--tctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag--------------------------------------------

upper sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 5'ss of exon 3
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattt--tggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag
||| || || ||||  || ||| | || ||||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| || || ||||| ||    | || ||||  | ||   |||   ||  || |  | |||||      |   | ||  || |  || ||      | ||    |||                                 
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATACCCCAGgtattgctgtcggtgtttttctgt-tgctattctttaatgtaatagatcagatgactaaccattaattactgttttt------tacccttgtggacag-----------------------------

upper sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag
||| || || ||||  || ||| | || ||||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| ||||| ||    | || ||||     |||  |   || |  |  | |||||      |   | ||  || || || ||      | ||    |||                                 
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaaccattaattaccgttttt------tacccttgtggacag-----------------------------

upper sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ16947 (Selaginella moellendorffii), 5'ss of exon 3
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag
|||||| ||||||||||||||    || || || ||| | || || ||||||||||| ||||| ||||||||||| ||| | || ||||| |||||||||||       |||| |||  | | |   || |  |  |  | | ||   | || ||  |                                                                   
TCCAAAGGGCCAGGGCCAGAACGTCCAGGCTCAAATGCTTTCGGACCCAAACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgt-------ttggcgttccaaaat---cttgtctcgg--tctcgacgtttcttttccag------------------------------------------------------------------

upper sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ16068 (Selaginella moellendorffii), 5'ss of exon 3
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtac-tttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag
|||||| ||||||||||||||    || || || ||| | || || ||||||||||| ||||| ||||||||||| ||| | || ||||| |||||||||||       |||| |||  | | |   || | | | | | | |   ||   | | |  | ||| |||  ||                                                       
TCCAAAGGGCCAGGGCCAGAACGTCCAGGCTCAAATGCTTTCGGACCCAAACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgt-------ttggcgttccaaaat---cttg-tctcggtctcgagccaacttttcgggcgtttcttttgcag------------------------------------------------------

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|208135014|gb|GD926661.1|GD926661
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTAGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|192306569|gb|FG997239.1|FG997239
EST:     ACATGGCCATTGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|192312658|gb|FK004346.1|FK004346
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|193632589|gb|FK580521.1|FK580521
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTTCTTTTCTGGATTTGTAGCAGC
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTT-CTTTTCTGGATTTGTAGCAGC
EST: gi|193609755|gb|FK560755.1|FK560755
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|193451079|gb|FK415693.1|FK415693
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTT-CTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|192312657|gb|FK004345.1|FK004345
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|208142885|gb|GD941497.1|GD941497
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATCATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|192323021|gb|FK016752.1|FK016752
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|192294522|gb|FG987451.1|FG987451
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|17023264|gb|BM094298.1|BM094298
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTT
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTT
EST: gi|11274440|gb|BF324793.1|BF324793
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
EST: gi|7588400|gb|AW704196.1|AW704196
EST:     ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAG                         ACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG
genomic: ACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaat ... tttcccacagACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA