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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTAGAAGCACCCCCATCATGGGCTCCGGATGCCCTTGATGCTGCTGTGCAGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgtataatctttatgcaaattctaacctggggaatagttaagaaatcagaagtagaaagtattattgaaaaataaagcatttattatatcaaat...

Basic information

species Glycine max
transcript GLYMA09G07240.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G07240.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os01g08700.8 (Oryza sativa), 5'ss of exon 10
TTTAGAAGCACCCCCATCATGGGCTCCGGATGCCCTTGATGCTGCTGTGCAGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgtataatctttatgcaaattctaacctggggaatagttaagaaatcagaagtagaaagtattattgaaaaataaagcatttattatatcaaat-------------------------------------
| | || ||||| ||||||||||| || ||||| |||||||| || || |||||||| || || ||| |||| || |||||||| | || ||| ||  |||||     || | ||| | ||    || |  |   |  |  | | ||||   || |   |   | ||||||   | || |   ||||   | | |  |||                                     
TCTCGAGGCACCACCATCATGGGCCCCAGATGCACTTGATGCAGCAGTACAGCTTGTTGAACTCCTTAGAGCAGCGGAAGATTACGATTCTGGCATGCGGgtatatcataca-tctctctggctgttgtttcagtgctatcaatcaagatgacacat-catgcaatattatc--ataacagcacattatgtgttttgaatattttattgattgtcatagctttgttttatgttttag

upper sequence: GLYMA09G07240.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 9
TTTAGAAGCACCCCCATCATGGGCTCCGGATGCCCTTGATGCTGCTGTGCAGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgtata----atctttatgcaaattctaacctggggaatagttaagaaatcagaagtagaaagtattattgaaaaata-aagcatttattatatcaaat-------------------
| | |||||||| |||||||||||||| ||||| |||||||| || || ||||| || ||||| ||| |||| |||||||||||||||| ||| ||  ||||| |   ||      |  ||  |   | | | ||  |    | | |   |  |  || || |     |    |||      |  ||   || ||||  |   ||                   
TCTCGAAGCACCTCCATCATGGGCTCCAGATGCACTTGATGCAGCAGTACAGCTAGTTGAGCTACTTAGAGCAGCTGAAGATTATGCTTCTGGCATGCGGgtatgacatacttcacagattattttgagtgcaaaattatcaagttgcctacgatacaaaattgtccggccacatttgtgtgtgtaaattttcattaactgtgatacttttattttatttgtag

upper sequence: GLYMA09G07240.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G107101_T06 (Zea mays), 5'ss of exon 9
TTTAGAAGCACCCCCATCATGGGCTCCGGATGCCCTTGATGCTGCTGTGCAGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgtataatctttatgcaaattctaacctggggaatagttaagaaatcagaagtagaaagtattattgaaaaataaagcattta---ttatatcaaat---------------------
| | |||||||| |||||||||||||| ||||| |||||||| || || || || || ||||| ||| |||| || ||||||||||||| ||| ||  ||||| ||  ||    ||| |  || ||| |  | ||   ||| || |||    |     || ||| |  | |    | ||      || |   || | | || |                     
TCTGGAAGCACCACCATCATGGGCTCCAGATGCACTTGATGCAGCAGTACAACTAGTTGAGCTACTTAGAGCAGCCGAAGATTATGCTTCTGGCATGCGGgtatgccata----cttca--cagattatc-cttgcaaaattgtcaagttgcctatgatacaaaattgtctaaccacatctttggttcaactttttgttaactgtggcactttattttttgtag

upper sequence: GLYMA09G07240.1 (Glycine max), 5'ss of exon 9
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 5'ss of exon 8
TTTAGAAGCACCCCCATCATGGGCTCCGGATGCCCTTGATGCTGCTGTGCAGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgtata---atct-----ttatgc----aaattctaacctggggaatagttaagaaatcag--aagtagaaagtattattgaaaaataaagcatttattatatcaaat------------
 ||||||||||| || || |||||||| ||||| |||||||||||||| |||||||| || || ||||||||||||||||||||||| | |||  |||||||||||   |||   ||||     |||  |     ||  ||||    |    | ||||  |||  ||  |  |      | | ||  || ||   ||| || || | ||    |            
CTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTACAGCTTGTGGAACTCCTTCGAGCTGCTGAAGATTATGCATCTGGTGTAAGGgtaagcgtaatatgaatctcttaattaccctccagaaagctaattgtgtcccttgttataaaaaaagtcagctttggtatgtcatcaaagaaatcagctttgatcacattctttttcttggtgcag

upper sequence: GLYMA09G07240.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 5'ss of exon 10
TTTAGAAGCACCCCCATCATGGGCTCCGGATGCCCTTGATGCTGCTGTGCAGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgtataatcttta-tgcaaattctaacctggggaatagttaagaaatcagaagtagaaagtattattgaaaaataaagcatttattatatcaaat--
  | |||||||| |||||||||||||| ||||| ||||||||||| || |||||||| || |||||||| || |||||||||||||| |  || || |||||||| | ||| ||||  | |||||   || |  |  |   | |||   |   ||| |     || |   ||| |  | |   |||||  |||  ||   |  
ACTGGAAGCACCACCATCATGGGCTCCAGATGCTCTTGATGCTGCAGTACAGCTTGTGGAACTTCTTCGGGCAGCTGAAGATTATGCATCAGGCATGAGGgtaagttctattatctccactgcaacgacttaaatatgttct-gttgctatgccagtaaactcaaattgaattcagcatt--tgcattctttaattcttttgg

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|120531323|gb|EH259456.1|EH259456
EST:     AGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGG                         CTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCA
genomic: AGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgta ... gttaatacagCTTCCTAGAAATTGGATGCATTTTCATTTCTTGCGTGCTATAGGGACTGCA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTAGAAGCACCCCCATCATGGGCTCCGGATGCCCTTGATGCTGCTGTGCAGCTTGTAGAGCTTCTTCGAGCTGCTGAAGATTATGCTTGTGGAATAAGGgtaagctgtataatctttatgcaaattctaacctggggaatagttaagaaatcagaagtagaaagtattattgaaaaataaagcatttattatatcaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataaa