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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttaccatcaagttctctgtgcacagtttctgaatgaaaacatttcggcattaaaacatatagttgtgtatactggagctctataacttccttttt...

Basic information

species Oryza sativa
transcript LOC_Os02g32570.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G057504_T01 (Zea mays), 5'ss of exon 7
GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttaccatcaagttctctgtgcacagtttctgaatgaaaacatttcg---gcattaaaacatatagttgtgtatactggagctctataacttccttttt
|||||||||||||| ||||| ||||| ||||||||||| || || ||||| || |||||||||||||||||||||||   ||||  |  | ||| |||   |||||  ||  |||| |  |     |||    ||| ||| | ||   |   || |   | | |      |    
GTTCTGCTTATGTCTCTGAAGGCTGGAGGTGTTGGAATCAATCTTACTGCCGCTTCTAATGCATTTGTCATGgtatgcc-ccattgaact-tctttgctgcgtttccaaacaaaaaaaacttatgtgcaaatcaacctattggtgcaaaccatgcaaaccaacacaagaatgga-

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA12G30540.1 (Glycine max), 5'ss of exon 19
GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgtta--ccatcaagttctctgtgcacagtttctgaatgaaaacatttcggcattaaaacat---atagttgtgtatactggagctctataacttccttttt
||  || | ||||| || ||||||||||| || || ||||||||||| || || |||||||| |||||||||||| || |  | ||    |   |    | ||       | || ||  | || |   |   |  ||   || | | |  ||| |||     ||| |    | |   
GTGTTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgaaactattttttaaccaaatcgcatggggatagtgtaataaatttgaactcggataattggattgctatcaatattggg----tatgatccacatga-

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA17G05390.1 (Glycine max), 5'ss of exon 18
GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttaccatcaagttctctgtgcacagtttctgaatgaaaacatttcggcattaaaacatatagttg--tgtatactggagctctataacttccttttt
|| ||| | ||||| || ||||||||||| || || ||||||||||| || || |||||||| |||||||||||| ||    |     || |      |     |  | || ||      |     | ||  |  ||| |||  | | ||       |   ||   |||     
GTGCTGTTAATGTCACTAAAAGCTGGTGGAGTAGGTATAAACCTAACAGCAGCTTCTAATGCTTTTGTCATGgtacgtgcaaactgttttttaaccaaatcacatggggataaagtgtaataaatttgaactctgataattggatttctatcaacattgggtatgatccaca--

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 5'ss of exon 18
GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttaccatca-agttctctgtgcacagtttctgaatgaaaacatttcggcattaaaacatatagttgtgtatactggagctctataacttccttttt---
|| ||| | ||||| || ||||||||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||||||  |     | || | ||| || |   |      || |     | | ||  ||| | ||| || | |   || |   |     | ||     |  |    
GTACTGTTGATGTCTCTAAAAGCTGGTGGCGTTGGGATAAATCTAACAGCTGCGTCCAATGCTTTTGTCATGgtatggaatatctatagatatctatgaaagatc---atatcagtttctataggatttagaccatgtaatagctcat-ccaaaatatgaaaatcgagtagtagtt

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 5'ss of exon 18
GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttaccatcaagttctctgtgcacagtttctgaatgaaaacat--ttcggcattaaaacatatagttgtgtatactggagctctataacttccttttt--
||  |||| |||||  |||| |||||||| ||||||||||||||||| |||||||| ||||| |||||  ||||||||    |  |  | |    |   ||  || | |||    || |  |   |     |    |   |   | |||||   || |  | | | |     ||  
GTCTTGCTAATGTCGTTGAAGGCTGGTGGAGTTGGAATAAACCTAACGGCTGCATCCAATGCCTTTGTTTTGgtatgtactga--agatccaaacttttcacctttttaattgtgacgtgatatagtgcctagttgtg-ggcactatatacaatag-tagaaagcattggcattag

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|88197570|gb|CI197420.1|CI197420
EST:     CTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG                         GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
genomic: CTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttacc ... tttccttcagGATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
EST: gi|89178965|gb|CI043470.1|CI043470
EST:     TGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG                         GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
genomic: TGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttacc ... tttccttcagGATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
EST: gi|88837636|gb|CI078996.1|CI078996
EST:     GCATCTAATGCATTTGTCATG                         GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
genomic: GCATCTAATGCATTTGTCATGgtatgttacc ... tttccttcagGATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
EST: gi|86479033|gb|CI121666.1|CI121666
EST:     CTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG                         GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
genomic: CTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttacc ... tttccttcagGATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
EST: gi|89180507|gb|CI044786.1|CI044786
EST:     GGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATG                         GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT
genomic: GGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttacc ... tttccttcagGATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTGCTTATGTCCCTGAAAGCTGGTGGTGTTGGAATAAACCTAACTGCTGCATCTAATGCATTTGTCATGgtatgttaccatcaagttctctgtgcacagtttctgaatgaaaacatttcggcattaaaacatatagttgtgtatactggagctctataacttccttttt

- - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - -  TGCTGC