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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttat-tacgtactaattatttaccatgtatattctaagccg-ttgatttgaatgcag
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || || |||||||||||||||||| |||||  | | |||| ||| |    |  | ||||   ||| | || ||||||  |  ||| || |  |||||
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgta---atattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag
||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| || || ||||| || ||||| ||| | ||||| |||||| |||||||||   | ||  || ||          | | |  ||  |  | ||||    |   |  |  | ||   |  |||   || ||
AAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTATATGgtatggaaataaatcattcccacaaattcagtgtgtg-tggtcatttgtactagcttgttgatgcttcttttttctttgtag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaat---attcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag
||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || || ||||| ||| | |||||||||||| ||||||||||    ||  || ||          |   |  ||  | ||  |||    |   |     | ||   |  ||||  || ||
AAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTATATGgtaaggaaataaatcattcccacaaattcggtgtgtg-tgatcgtttgtactagcttgctgatgcttcttttttgtttgtag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgt-actaattatttaccatgtatattctaagccgttgatttgaatgcag
||||||||||| ||||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| ||||| ||| |||| ||||||||| |||||||||| |   ||||  || ||    |   |   | |    ||   | |    |   |  |   | | ||||          
AAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTATATGgtaagaaaaatgagattttacaaatctctctttcatcttttgcctgctgactgcttatttctctgatgatag--------

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag
|||||||| |||||| | || || || ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||| || | || || ||||| ||||||||     |||   ||   |||   |||  |  ||    |  ||   | | | | || | | | | | |||| |  ||
AAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATCTATGgtaaggcagatggagtttacttgcagattgggccctccccagctaagttctctttgctga-ctgcttaattgattttag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag----------------------
||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||| |  ||| |||||| | |||||  | | |     |  | |    | |  || |   | |   |  ||  ||   ||  |  ||| |  ||                      
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgta-tgttcattttttaaatggaggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 5'ss of exon 22
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatctta-------tattggttattac-gtactaattatttaccatgtatattctaagccgttgatttgaatgcag---------------
||||| || |||||||| ||||| ||||| ||||| || ||||||||||||||||| |||||        |   ||| ||||| |||||||||||  |||||    |||||    |||        ||   || | |  ||   | | || | |  |||   |   |  || | | |      |  |               
AAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATTCATGgtg-cgttcattcaattaatggaggcatcccttctcattgtctcagtcatctgct-tgtggttgaaacaccatggttactggggttgtgggtgctttaagag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgta-----at---attcatgatcttatatt---ggttattacgtactaattatt--taccatgtatattctaagccgttgat-ttgaatgcag--------------------------------------------------------------------------
||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||||||| ||||||| ||  ||||||||      ||   ||  | | ||  || ||     | ||| |    || || ||  |   | | | |     |||   || | ||   |  |                                                                           
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: EFJ33980 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag
||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||  |||  |||||||  |||| ||||| ||  | || ||| | |   |  || || | |||  | |  ||  |   ||    || || | | ||| |                    
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgaga---acaattttgttttgtgtctagcgagcggttttgacacaat-tctcttcgattgtaacag-----------

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
lower sequence: EFJ37488 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatat---tggttatt-------acgtactaattatttaccatgtatatt--ctaagccgttgatttgaatgcag-----------------------------------
||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||   ||  |||||||  |||| ||||| ||  | || ||| | |   ||  | || | |   | |  | |        || |   ||   |  |    ||   |  | |||   |     |   ||                                      
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgagaacaattttgttttgtgtctagcgagtccacctggcgaaaggatcggtcgctgaatagcatggcaaagttttctccctatgtgtgactcggttttgacacaattctcttcgattgtaacag

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|66919239|gb|CX106087.1|CX106087
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29671404|gb|CB667679.1|CB667679
EST:     CAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: CAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|58590451|gb|CF988759.1|CF988759
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|58595336|gb|CF993644.1|CF993644
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29679208|gb|CB675483.1|CB675483
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29679210|gb|CB675485.1|CB675485
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29665943|gb|CB662218.1|CB662218
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29665942|gb|CB662217.1|CB662217
EST:     TGAGAATGTCTATGTTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29674249|gb|CB670524.1|CB670524
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29670549|gb|CB666824.1|CB666824
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTNTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
EST: gi|29622335|gb|CB627346.1|CB627346
EST:     GTTTATTGCGCAGTGCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG
genomic: GTTTATTGCGCAGTGCTTTATATATGgtaatattca ... ttgaatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGAGG