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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatcccatcatgtccttgctttttttttagagaggggaaattcctccatccttggttacatggaagttgcttttgttagataaggtttccatgctt...

Basic information

species Oryza sativa
transcript LOC_Os02g47600.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47600.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G046587_T02 (Zea mays), 5'ss of exon 6
GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaat---cccatcatgtccttgctttttttttagagaggggaaattcctccatccttggttacatggaagttgcttttgttagataaggtttccatgctt
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||  | |    || |||  |  | || |  | |||     |   |  ||   ||||  ||  || |   | | ||  |      |  | |  | |   |    
GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAGgtctagtgtctccgtcacctgatcgcatagtgtttgctatgtttaccttagaccatattttttttccgtgtaatt-ttgagaccacttgacatgttagttt--

upper sequence: LOC_Os02g47600.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 6
GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatcccatcatgtccttgctttttttttagagaggggaaattcctccatccttggttacatggaagttgcttttgttaga--taaggtttccatgctt----
||||  ||  | ||||| |  ||||| || |||||||||||||| || |||||||||||||| ||||| |||   |  |   |||||||||| | |||       | |      |    |  ||   |  ||   ||   || ||  | |  | |     | |  | |    
GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc-cctcctccttgctttctgtttttcatttgca-----ttgggacaatgaagaagtgagggtctattctgaaaaaatttaaaaggctacccattaaa

upper sequence: LOC_Os02g47600.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G37790.1 (Glycine max), 5'ss of exon 6
GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatcccatcatgtccttgctttttttttagagaggggaaattcctccatccttggttacatggaagttgcttttgttagat----aaggtttccatgctt--
||||  ||  | ||||| |  ||||| || |||||||||||||| || |||||||||||||| ||||| |||      |   |||||||||| | |||       | |      |  | |  ||   |  ||    |   || ||  | |     || |     | || |  
GAACCCGTGCTTCCTGGTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagtt-gcctcctccttgctttctgtttttcatttgca-----ttggaacaatgaagaagtgaggatcttttctgaaaaaacataaaaggcattaagcattt

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|163918159|gb|EG715273.1|EG715273
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|163925750|gb|EG714586.1|EG714586
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|163926919|gb|EG715144.1|EG715144
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|58601442|gb|CK011970.1|CK011970
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|8404630|gb|AU091984.1|AU091984
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|16753343|gb|BM037722.1|BM037722
EST:     CCTATGATTTGATCAG                         GGTGAGAAAGATGACAAGATCATACCTGTTTGTGCTGATGACCCTGAATA
genomic: CCTATGA-TTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATA
EST: gi|15852955|gb|BI805751.1|BI805751
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|58689221|gb|CK077908.1|CK077908
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|163928605|gb|EG710890.1|EG710890
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTCGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATA
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGT-GAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATA
EST: gi|58688425|gb|CK077112.1|CK077112
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|58596788|gb|CK007316.1|CK007316
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatcccatcatgtccttgctttttttttagagaggggaaattcctccatccttggttacatggaagttgcttttgttagataaggtttccatgctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcctcc