Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCGTCGAATCCTTTCGGGCCTCCCGGGCTCCTGCTTCTCCTTCGTGCACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgccaccctatttatctcttcgtttctgtgtgcttagcctaggcgttgctccaccctttggagcttcatttcatattcctgcgaggctgatcc...

Basic information

species Oryza sativa
transcript LOC_Os01g22390.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g22390.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G118641_T01 (Zea mays), 5'ss of exon 1
GGAGCGTCGAATCCTTTCGGGCCTCCCGGGCTCCTGCTTCTCCTTCGTGCACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgccaccctatttatctcttcgtttctgtgtgcttagcctaggcgttgctccaccctttggagcttcatttc--atattcctgcgaggctgatcc--
|   || |   ||||    | |||| | |||||| || ||||||||||  ||||||||  ||| || || |||||||||||| || |||||||||| |||||    ||||  |       | |||||  | |||| | |||  |    |    |||||      |||   ||    | |     |||  |   |    | |   
GAGACGCCTTGTCCTACGTGACCTCGCCGGCTCCGGCCTCTCCTTCGTCTACGGCCTCTCCGACTCACCGCTCCCCTTCGCCGCCTCCGCCGTCGTTCAGgt----ccgcgtcgactcccacctctttatctctgggcgctctggtcggcatgtgctctcaaaattgttcctaggctcctagctttctcgtccgttcaaacgcg
















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|88354097|gb|CI636295.1|CI636295
EST:     ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAC                         ATTGCATCTGATGGGGCTGA
genomic: ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgc ... ggtattgcagATTGCATCTGATGGGGCTGA
EST: gi|88330251|gb|CI658560.1|CI658560
EST:     ACGGCCTCCACGACTCCCCTCTCCCCTTCCCCTCCGCCGCCGTCGTCCAG                         ATTGCATCTGATGGGGCTGAGGAATGTAA
genomic: ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgc ... ggtattgcagATTGCATCTGATGGGGCTGAGGAATGTAA
EST: gi|88349016|gb|CI654060.1|CI654060
EST:     ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAG                         ATTGCATCTGATGGGGCTGAGGAATGT
genomic: ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgc ... ggtattgcagATTGCATCTGATGGGGCTGAGGAATGT
EST: gi|88340963|gb|CI638519.1|CI638519
EST:     ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCCTCCAG                         ATTGCATCTGATGGGGCTGAGGAATGTAATGGGAGCC
genomic: ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgc ... ggtattgcagATTGCATCTGATGGGGCTGAGGAATGTAATGGGAGCC
EST: gi|88393107|gb|CI616591.1|CI616591
EST:     ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAG                         ATTGCATCTGATGGGGCTGAGGAATGTAATGGG
genomic: ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgc ... ggtattgcagATTGCATCTGATGGGGCTGAGGAATGTAATGGG
EST: gi|88340108|gb|CI650555.1|CI650555
EST:     ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAG                         ATTGCATCTGATGGG
genomic: ACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgc ... ggtattgcagATTGCATCTGATGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCGTCGAATCCTTTCGGGCCTCCCGGGCTCCTGCTTCTCCTTCGTGCACGGCCTCCACGAGTCCCCTCTCCCCTTCGCCTCCGCCGCCGTCGTCCAGgtctttccgccaccctatttatctcttcgtttctgtgtgcttagcctaggcgttgctccaccctttggagcttcatttcatattcctgcgaggctgatcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccacc