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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaactgttggattatgcttgcag

Basic information

species Glycine max
transcript GLYMA07G29500.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 5'ss of exon 5
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttctta----aactgttggattatgcttgcag------
 ||||||||||| ||||| || ||| | || || ||| |||| |||||||||||||||||||||||||| || ||||| |||||| ||||||||||||| ||  || | |||     |   |  |||  ||   || | |    ||  | |||  |||    ||||| | ||| ||  |           
TGATGTGTGGTCGTGTGGAGTAACCCTCTACGTAATGCTGGTTGGTGCATATCCTTTTGAGGATCCAGATGAGCCTAAGAATTTCAGGAAGACAATTCAGgtttcc-attgcggtcatccaacatcacggtctcaaaatttcataaccattttgattacaaaaactgatcgatgatcttcattttcgcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 5'ss of exon 7
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaactgttggattatgcttgcag--------------------------
 ||||| ||||| ||||| |||||  ||||||| ||| | || |||||||||||||| ||||||||||| || ||||| || ||||| || |||||||| || |  || |      | ||        ||   |  | | |||| |  |||||| | |  || | |   | ||     ||                          
TGATGTATGGTCCTGTGGTGTGACTCTATATGTTATGGTAGTTGGTGCATATCCTTTCGAGGATCCAGAAGAGCCTAAGAACTTCCGTAAAACAATTCAGgttatataatttcttttcttatttctcttgctttgtttacattggagcacttttttcatcct-tggctctctgtgaaaagctgatgtcagtgtcatttttgtgcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G066867_T01 (Zea mays), 5'ss of exon 6
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaa--ctgttggattatgcttg-cag
 ||||||||||| ||||| || ||  | || || ||| |||| ||||||||||| |||||||| ||||| || ||||| |||||| ||||||||||||| ||  |||       |   ||||   ||  ||      | |      | |   |  | |||  |||  |   | |||||| |||
TGATGTGTGGTCATGTGGAGTAACGCTGTACGTGATGCTGGTCGGTGCATATCCATTTGAGGACCCAGATGAGCCTAAGAATTTCAGGAAGACAATTCAGgtttcctttgcagactggtttacaccagcgtctctcaattgactgctcatcctgatcaaacgctgacgagatctgcttggcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G138861_T01 (Zea mays), 5'ss of exon 8
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctact-------gcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaactgttggat-tatgcttgcag--------------
 || || ||||| ||||| || ||| | ||||| ||| | || || |||||||||||||| |||||||| || ||||| || ||||| ||||||||||| || | ||  |       |||    |   || | |||| |  || | |    |  ||||| | | |   | | | |  ||||  ||                 
TGACGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGTTGTTGGCGCATATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatctttttttttcagcatgggtacaagttgaatgca-caagagtgcacacgtacttctgtcag-ttatagcacatatgtgtgtgtcctagcacgcaccc

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 7
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattactt-ttcttaaactgt-tggattatgcttgcag--------------------
 ||||| ||||| ||||| || ||| | ||||| |||   || ||||||||||||||||| || ||||| || ||||| || ||||| ||||||||||| || |  |  |    | ||  | | |  | || | |   | |    |  ||    |  |  || || |   |     |  |||                    
TGATGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGCTGTTGGTGCATATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttatttttttt--ctttcatggatacaagttgaatgcacaccagagcacgcgcttgtgtacagtgtatgtgtcaatcacagcacatatgtgtcctagcaca

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: AT4G33950.1 (Arabidopsis thaliana), 5'ss of exon 7
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaa-actgttggattatgcttgcag-------------------------
|||||| |||||||||||||| ||  | ||||||||| |||| || ||||||||||| || ||||| |||||||| || |||||| |||| || || ||||| | |   | |||  | || | |      ||||   || ||  |||||    | |||  |||       ||  ||  | |                         
AGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTATACATgtgagcc-tttcactttcttcatgcttcaatagttgaaaaatgtaattatggattttattacttgctagctaaactatctgttctcttgtgaaaatatttgctcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 7
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaactgttggattatgcttgcag
|||||| |||||||||||||| ||||||||||| ||| |||||||||| || || |||||||| || ||||||||||| || ||||  |||||||| || |||   | |     |||  |||   || | | | |     ||||||       | |||||   |||  |  | |||||||
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgta-tttgcgcaggcataattactgca-tatggcagctcaattgaa-----aattttaaatgattgtttgtttcttgcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 5'ss of exon 7
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtca--------atgtagtaataatattgaattactt-ttctta--aactgttggattatgcttgcag-------------------
 ||||||||||| || || |||||||| || |||||||||||||| ||||| || || ||||||||  | || || |  |||||| |||| || |||   || |  |     |   |||   ||| |         | | ||  |   |  || | | |  |||  |  ||||   ||||| |     | |                   
GGATGTGTGGTCGTGCGGTGTGACCTTGTACGTCATGTTGGTGGGAGCATACCCATTCGAGGATCCCTATGACCCAAGGAATTTCAGGAAAACCATTGGAgtgagttcgcataagttttgatggtaacatttggtgtttcgtggtttaaccgattcattcattcacagcaactcacggattgttgaaactgtgtttggcttggtttgcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 5'ss of exon 7
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaactgttggatt----atgcttgcag----------------------------------
||||||||||||||| || || ||||| || || |||||||| || ||||||||||| |||||||| || || || |  |||||| |||| || |||   ||||  |    ||||  |||| |||  | ||  |  |        ||  | | |    |   || | |||    |  | | ||                                   
AGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGGgtaagat----cacctcttttgggtttaagtttttgtgcagcgtgatgtcgtctgcgcattcgtcgaattcgataaaccttcacggaatgcctaagctgtgactggcttggtttgcag

upper sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 5'ss of exon 7
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgca----ccatttttaggtcaatgtagta-ataatattg--aattacttttcttaaactgttggattat-gcttgcag--------------------------------
 ||||||||||| ||||| |||||||| || || ||||| ||||| |||||||| ||||||||||| || || || |  |||||| |||| || |||   || |  |  || |      | || ||      |||| |  | || | |   |||    ||    |   |  || ||  | |||| | |                                
CGATGTGTGGTCGTGTGGAGTGACCTTGTACGTGATGTTAGTGGGGGCATATCCGTTTGAGGATCCCGATGACCCAAGGAATTTCAGGAAAACCATTGGGgtgagttcatgtaaattttaattgtaaagttttgtattgcacaacactaccaatcctgttgtcgattttaatgaatggttgcttacggaatgatgaagctgttgttgccttggtttgcag

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|254328433|gb|GR835398.1|GR835398
EST:     ATCC-TTTGAGGATCCAGAGGAACCT-AAAATTTCCGGAAGACAATTCAT                         AGGA-TTTGAAAGTCCAGTACTCAATTCCTGATTATGTTCATATATCTTCT
genomic: ATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctact ... atgcttgcagAGGATTTTGAAAGTCCAGTACTCAATTCCTGATTATGTTCATATATCTTCT
EST: gi|24205189|gb|BU964442.1|BU964442
EST:     ATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCAT                         AGGATTTTGAAAGTCCAGTACTCAATTCCTGATTATGTTCATATATCTTCT
genomic: ATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctact ... atgcttgcagAGGATTTTGAAAGTCCAGTACTCAATTCCTGATTATGTTCATATATCTTCT
EST: gi|254328432|gb|GR835397.1|GR835397
EST:     ATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCAT                         AGGATTTTGAAAGTCCAGTACTCAATTCCTGATTATGTTCATATATCTTCT
genomic: ATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctact ... atgcttgcagAGGATTTTGAAAGTCCAGTACTCAATTCCTGATTATGTTCATATATCTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaactgttggattatgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA