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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAAACTGGATTTAAACCTGATGGAACACTACGAGAGGCATTGCCCTCCTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagatgatcctatctattttctcaaaattttgtcttatttagatcctactttgattgacttatgtgcacagaccgatcatttatacctatacttt...

Basic information

species Oryza sativa
transcript LOC_Os10g33720.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 5'ss of exon 4
GATGAAACTGGATTTAAACCTGATGGAACACTACGAGAGGCATTGCCCTCCTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagatgatcctatctattttctcaaaattttgtcttatttagatcctactttgattgacttatgtgcacagaccgatca--tttatacctatacttt
| |||| |||||||||||||||||||| ||||| ||||||||||||||||| ||||||||||| || || ||| ||||||| ||||||||||||||||||||| | |  ||||| || || || ||||||| | || | |||||   ||   |  |||  |||  ||| |   |       |    || |||     ||| |
GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactac-tgatc-taactcttctctcaaagtgttcttttattccaattagatcttgcatgagatatatcttcgcttgacttgagttcatagactgactat

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 5'ss of exon 3
GATGAAACTGGATTTAAACCTGATGGAACACTACGAGAGGCATTGCCCTCCTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagatgatcctatctattttctcaaaattttgtcttatttagatcctactttga--ttgacttatgtgcacagaccgatcatttatacctatacttt-
| |||| |||||||||||||||||||| ||||| ||||||||||||||||| ||||||||||| || || ||| ||||||| ||||||||||||||||||||| | |  ||||  ||  | || ||||||| | || | |||||   ||     ||||   |||  ||  || ||  ||| || ||||   |||| |  |   
GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactac-tgatt-taaatcttctctcaaagtgttcttttattccaattaggttttgtacttgttttgagttcatggactgagcatt-gcacctgttttgag

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 5'ss of exon 2
GATGAAACTGGATTTAAACCTGATGGAACACTACGAGAGGCATTGCCCTCCTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagatgatcctatctattttctcaaaattttgtcttatttagatcctactttgattgacttatgtgcacagaccgatcatt-tatacctatacttt------------
| ||||  |||||||     ||||||| ||||| ||||| |||||||| || |||||||||||||  || ||| ||||||| || |||   || || |||||    ||    | ||    | ||| |  |||| |||          |   ||  ||| ||   ||||   ||   ||| |  ||  |   | | | || |            
GTTGAAGTTGGATTTGTCTTTGATGGAGCACTATGAGAGACATTGCCCACCACCTGAAAGGCGCTATAATTGCTTGATTCCTCCTCCAGCAGGGTACAAGgt---gagtctgtgct--taagttttttgaaatattgggaccaaggaagtttatattgttttcattatccacatgtacctaagatgattctcttctgctgtgggcggtaacag

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S5_344V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGAAACTGGATTTAAACCTGATGGAACACTACGAGAGGCATTGCCCTCCTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagatgatcctatctattttctcaaaattttgtcttatttagatcctactttgattgactta--tgtgcacagaccgatcatttatacctatacttt-----
| ||||| || |      ||||||||| ||||| |||||||||||||||||||  ||    ||  |  | ||| ||||||| || || | |  ||| |||||  ||     || || |     || | ||       ||      ||||  |  |||  ||||   |   ||   | |      ||||||   || ||||       
GTTGAAATTGAACCACCCCCTGATGGAGCACTATGAGAGGCATTGCCCTCCTCAAGAGCACCGACTTCAATGCTTGATTCCTCCTCCTCCTAACTACAAGgtatcac----atactctgagcattttaaaggacagatcaatccaagatttt--tttagttgatggaaccgttttccgctattccatttagggct-tactcggattt

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|33675210|gb|CF303449.1|CF303449
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|27554159|gb|CA998059.1|CA998059
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|44676356|gb|CR289790.1|CR289790
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|163926509|gb|EG712373.1|EG712373
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|33676827|gb|CF305066.1|CF305066
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|33676729|gb|CF304968.1|CF304968
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|33797110|gb|CF324420.1|CF324420
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT

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: 71 (upstream exon), 55 (downstream exon)
Score: 6

GATGAAACTGGATTTAAACCTGATGGAACACTACGAGAGGCATTGCCCTCCTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG




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