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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgttttatactataaactcttaatttaatctaattattctataagcagatttcttggtataagctaattaagccatttctgtgttggtagccaaagg...

Basic information

species Glycine max
transcript GLYMA11G09790.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G09790.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G113995_T03 (Zea mays), 5'ss of exon 2
GTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgttttatactataaactc-ttaatttaatctaattattctataagcagatttcttggtataagctaattaagccatttctgtgttggtagccaaagg-
||||||||||||||||| |||||||| || ||||| || ||| |||||||||| || || || || ||||| || |||||||| || || |||  ||| | |  |  | | || || | ||  | |  |  || ||| |  |  || |  ||  |  |    |   ||| |  |   |  |||  |    |  
GTTGTGATGCTTGGTCTGGATGCTGCCGGTAAAACCACCATATTGTACAAGCTGCATATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggttatctgtttcagattccttcagtttttttgttagttttattaata--ttaccagggctccggatgtgctgccgtggcaaaggaggtttctgctgtg

upper sequence: GLYMA11G09790.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G011518_T03 (Zea mays), 5'ss of exon 2
GTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgttt--------------------tatactataaactcttaatttaatc--taattattcta--taagcagattt---cttggtata-agctaattaagccatttctgtgtt-ggtagccaaagg------------------
|| |||||||||||  | ||||| ||||| ||||| || ||||| || ||||| |||||||| |||||| | || ||||| ||||| |||||| || ||                     ||   ||||  | |   || || |  |  | |||  |  |   ||  | |   | ||  ||  |  | |||   || ||  | ||||  ||  |   | |                  
GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAGgtccgattgtaccacctatctgcttgtgcatttcataacttttggtttcaaccattgctaattacagttgtccaactctgcacctgccatgcaattgattcgtccgttcatatgtttagtgacagcatgcactttatcacattgtag

upper sequence: GLYMA11G09790.2 (Glycine max), 5'ss of exon 2
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgttttatactataaac-tcttaatttaatctaattattctataagcagatttcttggtataagctaattaagccatttctgtgttggtagccaaagg
|| || ||||| ||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||||||| | ||||||||||| ||||| |||  ||   ||     || | | || ||||  | |   | ||||     ||  | ||||   |   | | | | ||  ||||     ||  ||  ||    
GTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCGgtaggtcagattgctcaagcatttttattttttttgcgttttct-----catttatcttacaacgggtttactgagg-attttaaatttcttacacag---

upper sequence: GLYMA11G09790.2 (Glycine max), 5'ss of exon 2
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgttttatactataaactcttaatttaatctaattattctataagcagatttcttggtataagctaattaagccatttctgtgttggtagccaaagg-----------
|| || ||||| || || ||||||||||| ||||||||||| || |||||||| || |||||||||||||| ||||||||||| || || |||  | ||| |    |    | || |  |    | ||||||||       ||| ||      || |    |  |  |||||||   || | | | | |             
GTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTGgtaagctttctg--gttgttttttgagctg---tgattattctt------gatctcagaagctatgtagttggattcatttcttgttttggaacaagatttggatagatct

upper sequence: GLYMA11G09790.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 2
GTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgttttatactataaactcttaatt-taatctaattattctataagcagatttcttggtataagctaattaagccatttctgtgttggtagccaaagg---
|||||||||||||| || ||||| ||||| |||||||| |||||||||||  | ||||||||||||||||| || |||||||| ||||| ||| ||||  |  || |    | ||   | | || |   | ||  |       | ||  || | |      ||  ||      |  | |   |||||| |     
GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAATTGCACATTGGAGAAGTTTTGTCCACTGTTCCCACAATTGgtacgtt--aggctgttgttttttccctgtgatttttgtgtttcagctaataaatttatgcttttcctccatctagtggc--caatataactagccatatcttc

upper sequence: GLYMA11G09790.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 5'ss of exon 2
GTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgttttatactataaactcttaatttaatctaattattctataagcagatttcttggtataagctaattaagccatttctgtgttggtagccaaagg-----------------------------------------------------------------------------------------
||||||||||||||| ||||||| || |||||||| || || || || ||||| |||||||||||  || | || || ||||| || || |||     | | ||   | |||            | || |||||  ||   || |   | ||     ||| || |    |   ||||||        | |                                                                                          
GTTGTGATGCTTGGTTTAGATGCAGCAGGCAAAACCACCATCCTCTATAAGCTTCACATTGGAGAGATTCTGTCCACCGTTCCCACCATTGgta-aagtgacacatgacacttgccgcaggtcttgatgattct-caaatggagtgtctcgtcgttcctagttgaag-gtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcag

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|298170256|gb|HO018880.1|HO018880
EST:     ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG                         GTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
genomic: ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgtttta ... tgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
EST: gi|9820855|gb|BE556365.1|BE556365
EST:     ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG                         GTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
genomic: ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgtttta ... tgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
EST: gi|151397286|gb|EV267159.1|EV267159
EST:     ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG                         GTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
genomic: ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgtttta ... tgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
EST: gi|192303486|gb|FG995920.1|FG995920
EST:     ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG                         GTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
genomic: ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgtttta ... tgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
EST: gi|58016117|gb|CX702859.1|CX702859
EST:     CTGTACAAGCTCCACA-TGGAGAAAGTTTTATCTACTGTTCCTACAATAG                         GTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
genomic: CTGTACAAGCTCCACATTGGAG-AAGTTTTATCTACTGTTCCTACAATAGgtgcgtttta ... tgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
EST: gi|151405888|gb|EV275703.1|EV275703
EST:     ACTGTACAAGCTCCACATTGGAGAAGTCTTATCTACGGTTCCTACAATAG                         GTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
genomic: ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgtttta ... tgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
EST: gi|192334432|gb|FK024447.1|FK024447
EST:     ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG                         GTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG
genomic: ACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgtttta ... tgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAGgtgcgttttatactataaactcttaatttaatctaattattctataagcagatttcttggtataagctaattaagccatttctgtgttggtagccaaagg

- - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT