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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGAGTTTCTTGAACCCTCTGCTGCCCAGAAACTGGTGATTGGATTTGATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaaatgaagcttatgaagcatgaagtatgttcatgcgatcttctgtttcataatagtggtcctttcaaactattttgtatctaccatctccta...

Basic information

species Oryza sativa
transcript LOC_Os01g38620.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G142984_T01 (Zea mays), 5'ss of exon 2
AGTTGAGTTTCTTGAACCCTCTGCTGCCCAGAAACTGGTGATTGGATTTGATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaaatgaagcttatgaagcatgaagtatgttcatgcgatcttctgtttcataatagtggtcctttcaaactattt-tgtatctaccatctccta-
||| ||||||||||||||||| |||||||||||  |||| ||||||||||| |||||||| || || || |||||| |||||||||||||||| |||||||||||   || | || ||||    |||||| ||    | ||  | | || | |||||| || |||        |||   ||| || | |  ||||    |  
AGTCGAGTTTCTTGAACCCTCAGCTGCCCAGAAGTTGGTAATTGGATTTGACTGTGAAGGTGTTGATCTCTGCCGCAATGGTGCTCTCTGTATTATGCAGgtgagcaaaagt-aaccttagctggcatgatgttgtattatagggttttgt-tttcatgattgtgacatcacaaaaaactttatgcagcagccattcatttt

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G081924_T01 (Zea mays), 5'ss of exon 2
AGTTGAGTTTCTTGAACCCTCTGCTGCCCAGAAACTGGTGATTGGATTTGATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaaatgaagcttatgaagcatgaagtatgttcatgcgatcttctgtttcataatagtggtcctttcaaactattttgtatctac-catctccta--
||| ||||||||||||||||| |||||||||||  |||| ||||||||||| |||||||| || || || || ||| |||||||||||||||| |||||||||||   || | || ||||  |  ||||  ||    | ||  ||| |  |||||||| || |||  | |  |    |||   | | | |  ||| |      
AGTCGAGTTTCTTGAACCCTCAGCTGCCCAGAAGTTGGTAATTGGATTTGACTGTGAAGGTGTTGATCTCTGTCGCAATGGTGCTCTCTGTATTATGCAGgtgagcaaaagtaaaccttagcagtcatggtgttgtattatatgattt--tgtttcatgattgtga-catcgctctgtatgcagcagccatgcatttttctta

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0002g02690.t01 (Vitis vinifera), 5'ss of exon 4
AGTTGAGTTTCTTGAACCCTCTGCTGCCCAGAAACTGGTGATTGGATTTGATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaaatgaagcttatgaagcatgaagtatgttcatgcgatcttctgtttcataa-tagtggtcctttcaaactattttgtatctaccatctccta----
    || |||||||  || ||  |||    | || |||| ||||||||||||||||| || || |||||||| || |||||   ||| || ||||||||||||| |   | | |  ||||||     | |  |||| |   || | |||||| |||||||   |  |   |  | ||||    | |    |  ||    ||    
GAAAGACTTTCTTGTTCCATCCCCTGTAAGGCAATTGGTTATTGGATTTGATTGTGAGGGTGTTGACCTTTGTCGTCATGGAAGTCTTTGCATCATGCAGgtgatt---attcattcttatgccatgttagctatgat--agcaaacttctgcttcataagctggagaattccctaacttcaatctcatgaggataatttaagcc

upper sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0008g00650.t01 (Vitis vinifera), 5'ss of exon 2
AGTTGAGTTTCTTGAACCCTCTGCTGCCCAGAAACTGGTGATTGGATTTGATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagt---tcaaatgaagcttatgaagcatgaagtat--gttcatgcgatcttctgtttcataatagtggtcctt-tcaaactattttgtatctaccatctccta
| |||| || || || |||||| |||    |||| |||| ||||| |||||||||||||| || ||||| || ||||||||  | || |||||||||||||| | |   |    || | | | | | ||    ||| |  | | ||   ||  | | |     || | |  |||   |  || |||   || | | |  ||     
AATTGAATTCCTGGAGCCCTCTCCTGAAAGGAAATTGGTCATTGGTTTTGATTGTGAAGGTGTTGACCTATGTCGCCATGGAACACTTTGTATCATGCAGgtaattgactttcttggaccatgtta-gctcagagtctcagatgatagaattctgtctgcatgaagaattttccccattgaattatggagtttattcattc-----

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|218487804|gb|FG952787.1|FG952787
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|58594793|gb|CF993101.1|CF993101
EST:     --TGTGAAGGCGTA-ACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|218504651|gb|FG960768.1|FG960768
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|58655403|gb|CK044083.1|CK044083
EST:     ATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|27577966|gb|CB000661.1|CB000661
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|38473357|gb|CF957489.1|CF957489
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|58588638|gb|CF986946.1|CF986946
EST:     ATTGTGAAGGCGTAGACCTTTGCCGACATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|313080792|gb|HO213589.1|HO213589
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|58598824|gb|CK009352.1|CK009352
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|218483500|gb|FG948234.1|FG948234
EST:     ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAG                         ATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
genomic: ATTGTGAAGGCGTAGACCTTTGCCGCCATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA
EST: gi|218502513|gb|FG958404.1|FG958404
EST:     TTGTGAAGGCGTAGA-CTTTGCCGCCAATGGTGC-CTCTGTAT-ATGCAG                         ATTGCA-TTCCTGACGCTGTTTA-TTAGTTGATGCTATTGAGGGTGGGAAA
genomic: TTGTGAAGGCGTAGACCTTTGCCGCC-ATGGTGCTCTCTGTATCATGCAGgtgagttcaa ... tttttttcagATTGCATTTCCTGACGCTGTTTACTTAGTTGATGCTATTGAGGGTGGGAAA