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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGCTGATAAAATGGTTGCTGCTGCTAGTTCTCGTAATCCTACTCTAGCTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgttacccatttgagtggtttccctttacttgtttagttgtttattacccctatctcaaaatttgaaatgatttttttaaattgtattacactac...

Basic information

species Glycine max
transcript GLYMA08G03020.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G03020.1 (Glycine max), 5'ss of exon 17
lower sequence: LOC_Os03g15900.2 (Oryza sativa), 5'ss of exon 15
AGATGCTGATAAAATGGTTGCTGCTGCTAGTTCTCGTAATCCTACTCTAGCTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgttacccatttg--agtggtttccctttacttgtttagttgtttattacccctatctcaaaatttgaaatgatttttttaaattgtattacactac
 ||||||||||||||||||||||| ||||| ||||| |||||||| || ||| |||| |||||| | || || ||||| |||||||  || |||||||||||||    | |  |   |    |||| |  | | |  |  | |       |||   | |||||||   |||      |  |   ||                
TGATGCTGATAAAATGGTTGCTGCAGCTAGCTCTCGCAATCCTACGCTTGCTAGTGCTTTGACACGTCTGCAAAGGTGTGCATTCAGCGGTAGCTGGGAGgtatgcccttctgaaaagctgatggtattgcatcatcttataacactggcatttttcttatctcattgttt------acctccgtag---------------

upper sequence: GLYMA08G03020.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G012319_T02 (Zea mays), 5'ss of exon 16
AGATGCTGATAAAATGGTTGCTGCTGCTAGTTCTCGTAATCCTACTCTAGCTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatat---gttacccatttgagtggtttccctttacttgtttagttgtttattacc-cctatctcaaaatttgaaatgatttttttaaattgtattacactac-------------------------------
||||||||||||||||||||||||||| ||||| ||||||||||| || ||| | ||  |||||||||| || ||||| ||||| | ||| ||||||||||||       || |  |    | |   ||  ||||| ||||||||       | ||   |       | ||   |  | ||||| ||  ||    ||    |                                 
AGATGCTGATAAAATGGTTGCTGCTGCAAGTTCCCGTAATCCTACACTTGCTAGCGCTCTGACAAGGCTTCAAAGGTGTGCATTTAGTGGAAGCTGGGAGgtagggccgtttgcaaaggacaatttattttcttta-ttgtttagaaaaacttgacgatcgggagtgatatagtatgtcattttatttgatgcctttctgttttctctctctctattgtactgttaaacttgtag

upper sequence: GLYMA08G03020.1 (Glycine max), 5'ss of exon 17
lower sequence: AT2G07360.2 (Arabidopsis thaliana), 5'ss of exon 18
AGATGCTGATAAAATGGTTGCTGCTGCTAGTTCTCGTAATCCTACTCTAGCTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgttacccatttgagtggtttccctttacttgtttagttgtttattacccctatctcaaaatttgaaatgatttttttaaattgtattacactac-----
 ||||| ||||||||||||||||||||||||||||| |||||||||||||||||||| || ||  | ||||||||||| ||||| | ||| ||||||||||||||        ||||   ||||      ||  |  ||| ||| |||| |    | || |   |   |  ||  |       ||    |   |||         
GGATGCAGATAAAATGGTTGCTGCTGCTAGTTCTCGCAATCCTACTCTAGCTGGTGCATTAACTCGCCTCCAGAGGTGTGCATTTAGTGGAAGCTGGGAGgtataccac-tatatttcgctggtcgtatatt-ttgatttggttttttaattggacaatttgtga---tagaagtagggcacaaagcaatcccacaaagtaggta

upper sequence: GLYMA08G03020.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 5'ss of exon 18
AGATGCTGATAAAATGGTTGCTGCTGCTAGTTCTCGTAATCCTACTCTAGCTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgttacccatttgagtggtttccctttacttgtttagttgtttattacccctatctcaaaatttgaaatgatttttttaaattgtattacactac-----
|||||| ||||||||||||||||| || ||||||||||| |||||||| ||| ||||  ||||  | ||||| ||||| || |||| |||||||||||||||||| |||  |||| ||  ||     |  ||    | |||  ||| |||| |   |||   | | |  |   |   ||    |     | |||  || |     
AGATGCAGATAAAATGGTTGCTGCAGCAAGTTCTCGTAACCCTACTCTGGCTAGTGCAATGACTCGACTCCAAAGGTGTGCTTTCAGTGGCAGCTGGGAGgtataagtt-tccatctggttg---ctcacttgagaggttacatgtctattgcttgtattagagagtaaggggtaggttaagcatgacat-ttatcctgcctggc

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|209706851|gb|BW661487.1|BW661487
EST:     CTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAG                         ATTCGAATTATTGCTGCTCAAGCTCTTACAACAATGGCAATTAGATCTGGG
genomic: CTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgtta ... gaacatgcagATTCGAATTATTGCTGCTCAAGCTCTTACAACAATGGCAATTAGATCTGGG
EST: gi|209714012|gb|BW684461.1|BW684461
EST:     CTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAG                         ATTCGAATTATTGCTGCTCAAGCTCTTACAACAATGGCAATTAGATCTGGG
genomic: CTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgtta ... gaacatgcagATTCGAATTATTGCTGCTCAAGCTCTTACAACAATGGCAATTAGATCTGGG
EST: gi|24135995|gb|BU926505.1|BU926505
EST:     CAGGTGCCTTGACAAGGCTCCAGAGGTGTGCATTCAATGGCAGCTGGGAG                         ATTCGAATTATTGCTGCTCAAGCTCTTACAACAATGGCAATTAGATCTGGT
genomic: CTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgtta ... gaacatgcagATTCGAATTATTGCTGCTCAAGCTCTTACAACAATGGCAATTAGATCTGGG
EST: gi|120530335|gb|EH258468.1|EH258468
EST:     CTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAG                         ATTCGAATTATTGCTGCTCAAGCTCTTACAACAATGGCAATTAGATCTGGG
genomic: CTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgtta ... gaacatgcagATTCGAATTATTGCTGCTCAAGCTCTTACAACAATGGCAATTAGATCTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGCTGATAAAATGGTTGCTGCTGCTAGTTCTCGTAATCCTACTCTAGCTGGTGCCTTGACAAGGCTCCAGAGGTGCGCATTCAATGGCAGCTGGGAGgtatatgttacccatttgagtggtttccctttacttgtttagttgtttattacccctatctcaaaatttgaaatgatttttttaaattgtattacactac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG