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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtgcaacatgatgttatataaagtaattgccaggtcctgtacaatttgttcatctttcacctggtcctggtggatcaagt...

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 49
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
lower sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 32
CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtgcaacatgatgttatataaagtaatt-gccaggtcctgtacaatttgttcatctttcacctggtcctggtggatcaagt
||||||||||||||||| ||||||||||| || ||||| ||||||||||| |||||  | || ||||| || |||||||| || || ||||| |||||||  |   ||  |||   ||   |    |||  || |||  ||    ||   | ||||    ||| | |       |    |    |  | |      |
CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAGgtattattcacacagtgtt-gtattatccaatggcatgtaacttatcaagctgaggcctgatggattaggtggcacagccaaagagaatattagtgtgctt

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
lower sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 50
CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtgcaacatgatgtt-atat---------aaagtaattgcca------ggtcctg--tacaatttgttcatctttcacctggtcctggtggat--caagt----------------------------------------------------------
||||||||||||||| | |||||||||||||||||||| ||||||||||| ||||| || |||||||| || |||||||| || || ||||| ||||||  |||||| | ||| |  | ||   | |  ||  |||          || || |||  |      |||| |   | ||  || || ||| | ||| | |      |  ||  |||||                                                          
CAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAGgta--ttattcctagtgtacttccacattaacattcgtattcctttggggaactatttgtaaaatggcggtcttcattgcagatt-ttaatcatgcactttgcatgttttcattgcaagtgttttgtttattgagcattctttcctgtttacaatctgatctgccatcattatctcag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 52
CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtg--caacatgatgttatataaagtaattgccaggtcctgtacaatttgttcatctttcacctggtcctggtggatcaagt
||||||||||||||| |||| ||||| ||||| || || ||||| || ||||||||||| |||||||| || ||||| |||||| ||||||| |||||| |  ||| || ||  |  ||         |    | |||||| |      |    |  | | ||   ||    | |    | |    |   |   ||| 
CAAGAGCTTGCTGCTATATTTAAGAAGATTGGAGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGGATTACCCAATTGTACCCAAAGgta-agaattaatggtatatttgattgggggaaaagaaaataaagaagaaaggaaacacattgctatgcattttcttgtttggttggtaagaaagtggaag-

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 51
CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtgcaacatgatgttatataaagtaattgccaggtcctgtacaatttgttcatctttcacctggtcctggtggatcaagt-----
|||||||| |||||| |||| ||||| ||||| || || ||||| || ||||||||||| |||||||| || || || |||||| ||||||| |||||| |  ||| || ||| |  || |    |     | | ||   ||  |  |||      | | |    |  | | |    ||||  ||||  |  ||||     
CAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAGgta-agaattaatggtgtatttg-attgggggaaaagaaaataaaagggaaaggaaacacatagtgatgtattttcttgtttggt--tggta-agaaagtggaag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 5'ss of exon 50
----CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtgcaa--catgatgttatataaagtaattgccaggtcctgtacaatt-tgttcatctttcacctggtcctggtggatcaagt
    ||||||||||  ||| | || |||||||| |||||||||||||| |  |||||||||||||| || |||||||  || ||  |    || || ||||||    ||    |     | | |||  |   |||||   |    |   ||      |  |   |||| | |  |  |   ||||  || |  ||  |  || 
GAAGCAAGAGCTTGGGGCTATTTTTAAGAAAATAGGTGACAAACAAACTTCCACAATTGGTCTTTACGACCTCTACCACATCACAAAGTCATATCCAAAGgtaatagatatgactatgtatttcaagtctcaatgtttcctgttcttcatgaacaaacgagccaaattgtatgtacttacaacctcatcttaatgcttgtag-

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 21
CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt-----catcgtgaaagtgcaacatgatgttatataaagtaattgccaggtcctgtacaatttgttcatctttcacctggtcctggtggatcaagt----------------------------------------------------------------------
|| || ||||||||| |||||||||||||||||||||| |||||||| || |||||| | |||||||| ||||| || || |||||||||||||||||| | |||      ||| ||  | ||  || |  |  |||  |  ||| | |  || |   | |   ||| ||| | ||    ||      || |    |||                                                                        
CAGGAACTTGCTGCTATATTCAAGAAAATTGGTGACAAGCAAACATGCACTATTGGTTTATATGAACTATACCGTATTACTCAACTGTACCCCAAGgtaaactataaattgcatggtatatgtttaaaagaagtttaagt--agtgaatagcatgaggtttgttattggttgagctcgggccaaagattgctaacacaatgatctcttaattagatctatcttcctgtctactgcatttgccagaaagttaatttgtgatttctatttcag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 5'ss of exon 50
CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtgcaacatgatgttatataaagtaattgccaggtcctgtacaatttgttcatctttcacctggtcctggtggatcaagt-------------------------------
|||||||||||||| || |||||||| || ||||| || || || || |||||||||||||| || || || || || || || || || ||  ||||       |    ||| ||      |   ||  ||  ||  ||  |||||   ||  | ||||||| |||  | |||      || |      |    |                               
CAAGAGCTTGCTGCAGTGTTCAAGAAGATCGGTGATAAGCAGACTTGCACAATTGGTCTTTACGAGCTTTATCGTATCACACAGCTTTATCCTCAGgtgcgaagctt---gtgcaacgttttctccatcgtagttactgt--ttgcctattcacgcacaatttcttccccgttccttctttctttaatattttgctcacaacatgcatgctcattctaccttaccag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 49
lower sequence: PP1S131_18V6.1 (Physcomitrella patens), 5'ss of exon 50
CAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattattcatcgtgaaagtgcaacatgatgttatataaagtaattgc---caggtcctgtacaatttgttcatctttcacctggtc-ctggtggatcaagt----------------
|||||||||||||| || || ||||| || ||||| || || || |||||||||||||| ||||| || || || || ||||| || || ||  |||| |     | ||  |   | | |   ||| | || | |   ||  ||      | ||| ||| |       || |  |  |     || |||    |                      
CAAGAGCTTGCTGCAGTGTTTAAGAAGATCGGTGATAAGCAGACTTGTACAATTGGTCTCTATGAGCTATATCGTATCACCCAGCTATATCCTCAGgtgtggagcttatttt---atttctttatggt-ttctttgccgtgcttatgcgtaagtcgtgttctgcggactcttggtcgaaactttcactgacaaaatgcactcttttttctcaacag

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|58658439|gb|CK047119.1|CK047119
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|58601380|gb|CK011908.1|CK011908
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|58675157|gb|CK063844.1|CK063844
EST:     GGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTGGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|29680245|gb|CB676520.1|CB676520
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCCAG                         GTTGATATATTTG
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTG
EST: gi|218497579|gb|FG955134.1|FG955134
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|58677253|gb|CK065940.1|CK065940
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG                         GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGGACCTAT
genomic: GTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAGgtatattatt ... ctattttcagGTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTAT