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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattgctattgttcatttagcaattttgattttgttttcatatttttctctctgcctattttttttctccttgttttgataagacattttgctcttgtatag

Basic information

species Oryza sativa
transcript LOC_Os07g49270.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 17
CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattgctattgttcatttagcaattttgattttgttttcatatttttctctctgcctattttttttctccttgttttgataagacattttgctcttgtatag
|| |||||||| || ||||| ||| | |||||||| ||||| |||||||| |||||||| || |||||||| |||||||||||||| | |  |   ||| || | || ||||    | ||  |      |    | |||  |  | | |  | ||  || | |                         
CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaactagtg--gtttatgtggccatttgttgtgtgggtcatggatggattttctaacactgtctggtgtc--tgctctag-----------------------
















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|87023333|gb|CI272161.1|CI272161
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|58694980|gb|CK083667.1|CK083667
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|29671781|gb|CB668056.1|CB668056
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86513328|gb|CI155961.1|CI155961
EST:     GAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: GAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86481989|gb|CI124622.1|CI124622
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACCACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86437389|gb|CI119111.1|CI119111
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCGAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCGTGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|89169860|gb|CI110219.1|CI110219
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|33675288|gb|CF303527.1|CF303527
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGNGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|88221174|gb|CI221130.1|CI221130
EST:     GGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: GGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|29663750|gb|CB660025.1|CB660025
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86478852|gb|CI121485.1|CI121485
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTCCAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86477898|gb|CI120531.1|CI120531
EST:     GTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: GTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|8527210|gb|AU092025.1|AU092025
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86437366|gb|CI119088.1|CI119088
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|88273930|gb|CI394336.1|CI394336
EST:     CAGTCTGGTTTCTCTCATAGGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGA
genomic: CAGTCTGGTTTCTCTCATA-GGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGA
EST: gi|88966319|gb|CI119454.1|CI119454
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|87030186|gb|CI270196.1|CI270196
EST:     TTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: TTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86477978|gb|CI120611.1|CI120611
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|58695027|gb|CK083714.1|CK083714
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|218478545|gb|FG960299.1|FG960299
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCCAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|8527425|gb|AU092240.1|AU092240
EST:     AATTGCTAGGNAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AATTGCTAGG-AATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|163927650|gb|EG712446.1|EG712446
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86481726|gb|CI124359.1|CI124359
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86827161|gb|CI270859.1|CI270859
EST:     TGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: TGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86436955|gb|CI118677.1|CI118677
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|86477298|gb|CI119931.1|CI119931
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|163926592|gb|EG713608.1|EG713608
EST:     AAATTGCTAGGAATTCTGTGTACCGGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|87027426|gb|CI272191.1|CI272191
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
EST: gi|88966359|gb|CI119494.1|CI119494
EST:     AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAG                         TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC
genomic: AAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 53 (downstream exon)
Score: 37

CTGTGGAAGCTAAGTTCATGCGACCTATGTGAAATTGCTAGGAATTCTGTGTACCAGTCTGGTTTCTCTCATAGGCTCAAGgtatagattg ... tcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGACATTCACCAGACAAATGTTCCTCACATCAGGATTGAATTCCGACACACT




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