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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattcttctgagaataggtccatattgtgtatattcagaccttaagactcatattttgcttacgacacag

Basic information

species Oryza sativa
transcript LOC_Os11g05880.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G34000.1 (Glycine max), 5'ss of exon 5
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggg-----gattcttctgagaataggtccatattgtgtatattcagaccttaagactcatattttgcttacgacacag-----------
| | ||||| ||||| || |  ||||| ||||| || ||| ||||||||||   |||||| || ||||||||||||||||| ||||| ||||| || || ||  |     |||  || |  || | |  |  | || | | | ||||    ||   | | || |||    || |  |              
ACTTGGAGTGGAGAAACTCAACAAAGATGATGTTCAAAAGCTGCAGTGGGAGATTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATAGCAgtaagatgaagatgattgtaggattggtgctgtgttttttgtcttcattattttttaat-atctttcaaatatgtaattatacacgaacag

upper sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G17500.1 (Glycine max), 5'ss of exon 2
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattcttctgagaataggtccatattgtgtatattcagaccttaagactcatattttgct-tacg-acacag
  | ||||| || || || || ||||| ||||| || ||| | || ||||| | |||||| || ||||||||||||||||| ||||| ||||| ||||| ||  |    ||      |||  || || ||  | ||| || | |  || |     ||||     | |||    ||||
GCTTGGAGTTGAAAAACTAAGCAAAGATGATGTTCAAAAGCTACAATGGGAGGTTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATTGCTgtaagaccactgtca--aatttgttcacatattttatctttatattttcatttaaatatgcaattgtacttgaacag

upper sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G33590.1 (Glycine max), 5'ss of exon 5
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattcttctgagaataggtccatattgtgtatattcagaccttaagactcatattttgcttacgacacag------------------
| | ||||| ||||| || |  ||||| ||||| || ||| ||||||||||   |||||| || ||||||||||||||||| ||||| ||||| || || ||  | ||  || |  || | |  |  | || |   | ||  | | | |  | || | |  |   |   | | |                   
ACTTGGAGTGGAGAAACTCAACAAAGATGATGTTCAAAAGCTGCAGTGGGAGATTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATAGCAgtaag-atgattgtaggattggtgctgtgtttt---ttttttgtcttcattattcttttaatatctttcaaatatgtaattatacatgaacag

upper sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 5
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattcttctgagaataggtccatattgtgtatattcagaccttaagactcatattttgcttacgacacag
  | || || ||||| || || ||||| ||||| || ||| | || ||||| | |||||| || ||||||||||||||||| ||||| ||||| ||||| ||  |    ||   ||   |   | |||||| | ||| ||           |   ||  | |  |      ||||
GCTTGGTGTTGAGAAACTCAGCAAAGATGATGTTCAAAAGCTACAATGGGAGGTTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATTGCTgtaagaccactgtcgaatttgtttacatattttttattttttttttcatgtaaatatgctattgtacttgaacag

upper sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattctt-ctgagaataggtccatattgtgtatattcag---accttaagactcatattttgcttacgacacag
||| ||||| || || ||||| ||||||||||| |||| |||||||||||||| ||||||||| ||||||||||| ||||||||||| ||||| ||||| ||  | | |||   | || || |    |  ||    || ||  |   || || |     | || ||   | | |||   
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgttttgttcacttttaactcaagatattttgttcaacag--

upper sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 5
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattcttctgagaataggtccatattgtgtatattcagaccttaag-actcatat---tttgct--tacgacacag-----------------
||| || || || |||||||| ||||| ||||| ||||||||||| ||||| | |||||||||||| ||||| || ||||| ||||| ||||| ||||| ||  | ||   | | | | | |    |  ||  || |||| |      | | | | || |   | ||||  | | |  | |                 
ATTGGGTGTGGAAAAGCTTAGCAAAGATGATGTTCAGAAGATGCAATGGGAGGTTTTGGAGGCTAAGATTGGGAATTGGATTCATTTCATGCGGATTGCTgtaagaatatatgtcaaatttgcgggaatttaggtgtattaaatttgcatgcatttatgtatatctgctcttccaattctgttattttacataaacag

upper sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g02340.t01 (Vitis vinifera), 5'ss of exon 5
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattcttctgaga----ataggtccatat-------tgtgtatattcagaccttaagactcatattttgcttacgacacag-----------------------
|||||| || || || |||| |||||| ||||| ||||||||||||||||||| |||||||||||| |||||||| ||||| ||||| ||||| ||||| ||  || ||     |  |    |||||   || |       ||||| | |       |       | |||||| ||    |  |||                       
ATTAGGTGTGGAAAAACTTACTAAAGATGATGTCCAGAAGATGCAGTGGGAAGTTTTGGAGGCTAAGATTGGAAATTGGATTCATTTCATGCGGATTGCTgtaagggtttactaggaactggataggattatttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtacgtatttt-ctcttaatccagccatttcatcatgcttgtaacag

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|29665901|gb|CB662176.1|CB662176
EST:     AAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCG                         GTCAAACTACTACTAGCAGGTGAAAGAAAAATCTGTGACCAGATTTTTGAT
genomic: AAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattc ... tacgacacagGTCAAACTACTACTAGCAGGTGAAAGAAAAATCTGTGACCAGATTTTTGAT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattcttctgagaataggtccatattgtgtatattcagaccttaagactcatattttgcttacgacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG