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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtcttattttttttttattaagtcttcatttaaaagtgcaaaatccttaaacatatttgttcatctttcaacttcattcatgtgacaacacgaatt...

Basic information

species Glycine max
transcript GLYMA11G01380.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G011518_T03 (Zea mays), 5'ss of exon 2
GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtg-ggtcttattttttttttatt-----aagtcttcatttaaaagtgcaaa-atccttaaacatatttgttcatctttcaactt--cattcatgtgacaacacgaatt--------------------------------------
|| |||||||||||  | ||||| ||||| ||||| || ||||| || |||||||||||||| |||||| | |||||||| ||||| || |||  | |  ||     | | |  |     |  || | | ||     | |||  ||   |||  | | |||| || || |  || |  ||| ||  |||     |   |                                       
GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAGgtccgattgtaccacctatctgcttgtgcatttcataacttttggtttcaaccattgctaattacagttgtccaactctgcacctgccatgcaattgattcgtccgttcatatgtttagtgacagcatgcactttatcacattgtag

upper sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G113995_T03 (Zea mays), 5'ss of exon 2
GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtcttattttttttttattaagtcttcatttaaaagtgcaaaatccttaaacatatttgttcatctttcaacttcattcatgtgacaacacgaatt---------
||||||||||||||||| |||||||| || ||||| || ||| | |||||||| || || || || ||||| || |||||||| || |||||| |||  ||| | |||   |||    ||||| ||     ||  |  |   | || ||   |        | |   |    |   ||| |||      ||         
GTTGTGATGCTTGGTCTGGATGCTGCCGGTAAAACCACCATATTGTACAAGCTGCATATCGGGGAGGTTTTGTCGACTGTTCCCACGATTGgtaggt--tatctgtttcagatt---ccttcagtttttt-tgttagttttattaatat---taccagggctccggatgtgctgccgtggcaaaggaggtttctgctgtg

upper sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 3
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtcttattttttttttattaagtcttcatttaaaagtgcaaa---atccttaaacatatttgttcat--ctttcaacttcattcatgtgacaacacgaatt
|| || ||||| ||||| ||||| |||||||||||||| ||||| |||||||| ||||| ||||||||| | || |||||||| ||||| ||| ||||  |||  |     |||     ||  |||     | |  |   ||| |  |||   |||  | |    ||| || ||| | ||                
GTCGTTATGCTGGGTCTGGATGCGGCTGGCAAAACAACGATACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCGgtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttcttacacag-------------

upper sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 3
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtcttattttttttttattaagtct--tcatttaaaagtgcaaaatccttaaacatatttgttcatctttcaacttcattcatgtgacaacacgaatt
|| || ||||| || || ||||||||||| ||||||||||| || ||||||||||| |||||||||||||| || |||||||| || ||||||  |  || |  || |||| | |  | |  | |||    |   || || |  ||   |  |   ||||| | |    ||    || |         ||  |
GTCGTTATGCTGGGGCTGGATGCTGCTGGAAAAACAACTATTCTCTACAAGCTTCATATTGGAGAAGTTTTGTCTACTGTTCCCACCATTGgtaagctttctggttgttttttgagctgtgattattcttgatctcagaagc--tatgtagttggattcatttcttgttttggaacaagatttggatagatct

upper sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 2
GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtcttattttttttttattaagtcttcatttaaaagtgcaaaatccttaaacatatttgttcatctttcaact--tcattcatgtgacaacacgaatt---
|||||||||||||| || ||||| ||||| |||||||| ||||| |||||  | ||||||||||||||||| ||||||||||| |||||||||  ||     | || |||| |       | ||||    ||   |    || | | || | || |  || | || ||  |     || | || |  |  ||    
GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAATTGCACATTGGAGAAGTTTTGTCCACTGTTCCCACAATTGgtacgttaggctgttgttttttc--cctgtgatttttgtgtttcag---ctaataaatttatgcttttcctccatctagtggccaatataactagccatatcttc

upper sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 3
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 5'ss of exon 2
GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgg---gtcttattttttttttattaagtcttcat---ttaaaagtgcaaaatcc------------ttaaacatatttgt-tcatctttc----aactt-----cattcatgtgacaacacgaatt----------------------------------------------------------
||||||||||||||| | ||||| || |||||||| || || || || |||||||||||||||||  || | ||||| ||||| || ||||||     | |  ||     ||     | ||||| ||   |   || || |   ||             || ||  || |||| | |||| |     |||||     | || || |        |  ||                                                          
GTTGTGATGCTTGGTTTAGATGCAGCAGGCAAAACCACCATCCTCTATAAGCTTCACATTGGAGAGATTCTGTCCACCGTTCCCACCATTGgtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcag

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|5057972|gb|AI736448.1|AI736448
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298199192|gb|HO042555.1|HO042555
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298170232|gb|HO018856.1|HO018856
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298188565|gb|HO035258.1|HO035258
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298172316|gb|HO019356.1|HO019356
EST:     GAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: GAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|298185092|gb|HO030305.1|HO030305
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
EST: gi|192296463|gb|FG989828.1|FG989828
EST:     ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG
genomic: ACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTGgtgggtcttattttttttttattaagtcttcatttaaaagtgcaaaatccttaaacatatttgttcatctttcaacttcattcatgtgacaacacgaatt

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