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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagctctcccatgagtctgctattattcttcaatgaaattacagtcaccttttagtttgttgtcacttgatttcttcccacaccacccaattttc...

Basic information

species Oryza sativa
transcript LOC_Os07g43060.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G086805_T02 (Zea mays), 5'ss of exon 2
AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagctctcccatgagtctgctattattcttcaatgaaattacagtcaccttttagtttgttgtcacttgatttcttcccacaccacccaattttc---
||| |||||  ||||||| ||  ||||||| ||||| || |||||||||||||||||||||  | | | |||||| | |  |||| |||  | |    |       |||||  ||       | |||||  ||  |||  || |     |   ||  |     
AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgag--ccttgatctcccgt-atcctgcaatttgtttgtcct----cctcagtctgctgcattcgttttgtcttttttttttctctccacttatgtaagctgtgtc
















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|86530402|gb|CI170608.1|CI170608
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|55431294|gb|CV728661.1|CV728661
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|55431292|gb|CV728660.1|CV728660
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGG-GA                         --A-GTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|11610378|gb|AU166054.1|AU166054
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88838475|gb|CI375023.1|CI375023
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|58686363|gb|CK075050.1|CK075050
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGG-GA                         --A-GTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88833830|gb|CI077311.1|CI077311
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88376412|gb|CI535516.1|CI535516
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTTTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|33684821|gb|CF313060.1|CF313060
EST:     TAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: TAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|86423375|gb|CI060948.1|CI060948
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|8857385|gb|AU094703.1|AU094703
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88380030|gb|CI513620.1|CI513620
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88212631|gb|CI212271.1|CI212271
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCTCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|163919996|gb|EG709802.1|EG709802
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTCGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88382569|gb|CI535777.1|CI535777
EST:     GTGATGAATCCTGGTAGGANTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|163928022|gb|EG709470.1|EG709470
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|87019382|gb|CI279892.1|CI279892
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88976243|gb|CI024460.1|CI024460
EST:     GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAA-T--TG-                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: GTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagct ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGGTGAgtacgtagctctcccatgagtctgctattattcttcaatgaaattacagtcaccttttagtttgttgtcacttgatttcttcccacaccacccaattttc

- - - - - - GATGGA
- - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccacc