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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTGAGGGCGAGATCTAGGAGGGAGGCGTCCATGGGAGCTCGCTGCTCCAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgctctcgctctcgcattgggttgggtttgggggggggggggagggatttggttgctggtttcggatgtgcgcgtgttgatgatggagtggggt...

Basic information

species Oryza sativa
transcript LOC_Os03g61010.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G121826_T01 (Zea mays), 5'ss of exon 1
GAGGTGAGGGCGAGATCTAGGAGGGAGGCGTCCATGGGAGCTCGCTGCTCCAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgctctcgctc----tcgcattgggttgggtttgggggggggggggagggatttggttgctggtttcggatgt-gcgcgtgttgatgatggagtggggt
||| |   ||| ||     |   |   ||| ||||||| ||||||||||||||||||||||| ||||||||||| || | |||||| |||||| |||| |||| |   ||  ||| |     | |    || ||  | |     ||       | | |||  ||     | ||   | | || |  |  |     |         
GAGATCTAGGCAAGCGAGCGAGCGAGCGCGGCCATGGGTGCTCGCTGCTCCAAGCTCTCCGTCTGCTGGTGGCCTCCCCGCTTCAAATCGCCGATGCTCGgtacgcgcctaccgcacattgccaccgctggctgcctctccccaggattctccgtgttttttttaaccttctctcctcttgctctcgccgcgcgcgcccc-----

upper sequence: LOC_Os03g61010.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G177445_T01 (Zea mays), 5'ss of exon 1
-GAGGTGAGGGCGAGATCTAGGAGGGAGGCGTCCATGGGAGCTCGCTGCTCCAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgctctcgctctcgcattgggttgggtt--tgggggggggggggagggatttggttgctggtttcgg-atgtgcgcgtgttgatgatggagtggggt
     ||   |||||||||||| | | | || ||||||| ||||||||||||||||||||||| ||||||||||| || |||||||| |||||  |||| |||| |  ||   |   | | |||||     | |   |      ||       |  |||  |  ||    ||   |    |||  |  |      |  ||    
GCGTCTGCCTGCGAGATCTAGGCGAGCG-CGGCCATGGGTGCTCGCTGCTCCAAGCTCTCCGTCTGCTGGTGGCCTCCCCACTTCAAATCGCCAATGCTCGgtacgccgcctac---cgcacattgccaccgctccctctcctaggattctccgagttttctctctctcctcaccacactcgcccggcgccccgcgcctgattc
















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|88400057|gb|CI588361.1|CI588361
EST:     CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTG                         AGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgct ... tgacgtgcagAGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|58612070|gb|CK039782.1|CK039782
EST:     CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTG                         AGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgct ... tgacgtgcagAGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|88350694|gb|CI617549.1|CI617549
EST:     CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTG                         AGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgct ... tgacgtgcagAGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|88362294|gb|CI608685.1|CI608685
EST:     CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTG                         AGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgct ... tgacgtgcagAGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|58667566|gb|CK056252.1|CK056252
EST:     CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTG                         AGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgct ... tgacgtgcagAGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|58686808|gb|CK075495.1|CK075495
EST:     CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTG                         AGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgct ... tgacgtgcagAGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
EST: gi|58668832|gb|CK057518.1|CK057518
EST:     CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTG                         AGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT
genomic: CAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgct ... tgacgtgcagAGAATGGCGCCGCCGCGGACGACGGCAGCGGCGTGCCGGTGTTCGCCGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTGAGGGCGAGATCTAGGAGGGAGGCGTCCATGGGAGCTCGCTGCTCCAAGCTCTCCGTGTGCTGGTGGCCGCCGCACTTCAAGTCGCCGCTGCTTGgtatggtgctctcgctctcgcattgggttgggtttgggggggggggggagggatttggttgctggtttcggatgtgcgcgtgttgatgatggagtggggt

- - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtggg