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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagattgctattgttcatttagcaattttgattttgttttcatatttttctctctgcctattttttttctccttgttttgataagacattttgctcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGACATTCACCAGACAAATGTTCCTCACATCAGGATTGAATTCCGACACACT

Basic information

species Oryza sativa
transcript LOC_Os07g49270.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 17
gtatagattgctattgttcatttagcaattttgattttgttttcatatttttctctctgcctattttttttctccttgttttgataagacattttgctcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGACATTCACCAGACAAATGTTCCTCACATCAGGATTGAATTCCGACACACT
||||| | |    | ||| || | || ||||     |||| |   |           ||  |   |||| |  |  ||| | | |       | ||||||     |||| |||||||| |||||||||||||||| ||| ||||  || ||||||||||| ||||||||||||||||||||||||||| ||||||| |||||||||
gtataaacta--gtggtttatgtggccatttg----ttgtgtgggt---------catggatggattttctaacactgtct-ggtg------tctgctct-----agTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT

upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 17
------------------------------------------------------------------gtatagattgctattgttcatt-tagcaattttg----attttgttttcatatttttctctctgcctattttttttctccttgttttgataaga---------------cattttgctcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGACATTCACCAGACAAATGTTCCTCACATCAGGATTGAATTCCGACACACT
                                                                  | || |  |||| ||      | |  | || ||     |||   || |||  |   || ||     || |   |   |   |   |  |||| |               |||     |    |  ||      ||||||||   |||||||||||| |||||||    |||||||||||||||| |||||||||| |||||||| ||  || | ||||| ||    
gtgagtggcatttctttggccctggattggcaagtttacaatttcacattggaaaattaaaaacatgcatggcatgctgttaccttctatgactatattataacattaacttgtcaactcaatcacttatgataataaataaataaataaataaataaaaacaacaacaacaatacatagatttacaattcagGTGAGATGGATTGGACCAAACTACTACAAGAGAGGTCCACTTGGCAATGACATTCACAAGACAAATGTGCCTCACATGAGAGTTAATTTCCGCCATGAG
















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|58694980|gb|CK083667.1|CK083667
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|33675288|gb|CF303527.1|CF303527
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGNGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|218478545|gb|FG960299.1|FG960299
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCCAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|163927650|gb|EG712446.1|EG712446
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|163926592|gb|EG713608.1|EG713608
EST:     AAATTGCTAGGAATTCTGTGTACCGGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctgcctattttttttctccttgttttgataagacattttgctcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGACATTCACCAGACAAATGTTCCTCACATCAGGATTGAATTCCGACACACT
                          ttttgat  putative branch site (score: 4)
                                       ttttgctctt  putative PPT
         tattttttttct  TA-rich tract