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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAGATCGTCCTGATCTGACTGCCCCAGAAAGCTTACAGCTATACCTGGACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttccttatattttttaaccttttttatgccaagtgaatcatctttgctgtatgatcgtaaagctttgcttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g03070.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03070.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G070487_T04 (Zea mays), 5'ss of exon 2
GCGAGATCGTCCTGATCTGACTGCCCCAGAAAGCTTACAGCTATACCTGGACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttccttatattttttaaccttttttatgccaagtgaatcatctttgctgtatgatcgtaaagctttgcttcttgcag
  | |||||||||||||||||||| || ||||| ||||| ||||| || || ||  | ||||| || || ||| ||||||||||||| |  || ||||||||  ||||| ||  ||   ||   |  |  ||   |||||   ||  ||   || ||        | | |  | ||||||||
AAGGGATCGTCCTGATCTGACTGCACCTGAAAGTTTACAACTATATCTTGATACACGTGTTGAGCAGCTTAAAGTTGCTACAGAGCTTTGCCTTTGGCAGgtttgttccataacttgcgtattttaatccatat-aagtg--ccacattccttgaattgctactgaacataccatcttgcag

upper sequence: LOC_Os01g03070.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G093050_T03 (Zea mays), 5'ss of exon 4
GCGAGATCGTCCTGATCTGACTGCCCCAGAAAGCTTACAGCTATACCTGGACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcc-----ttatattttttaaccttttttatgccaagtgaatcatctttgctgtatgatcgtaaagctttgcttcttgcag
  |||||||||||||||||||||| || ||||| ||||| || || || || ||  | ||||| || || ||| |||||||||| ||||| || ||||||||  |||||     |||| | ||||||    || | | || | |  |  |    ||||  ||      ||   |       ||||||
AAGAGATCGTCCTGATCTGACTGCACCTGAAAGTTTACAACTGTATCTTGATACACGTGTTGAGCAGCTTAAAGTTGCTACAGAACTCTCCCTTTGGCAGgtttgttccattacttatgtattttaattaattctttaccca-tatacaaa---tgctacattccttgaattgtccctggattgcag
















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|58655699|gb|CK044379.1|CK044379
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|33678088|gb|CF306327.1|CF306327
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTATCTGGCAG                         GAGGCCTTTAGGTCTGCGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|2427680|gb|C72143.1|C72143
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGNAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|58657791|gb|CK046471.1|CK046471
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|33677589|gb|CF305828.1|CF305828
EST:     GAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: GAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|33678827|gb|CF307066.1|CF307066
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
EST: gi|58661569|gb|CK050249.1|CK050249
EST:     ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAG                         GAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG
genomic: ACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttcct ... cttcttgcagGAGGCCTTTAGGTCTGTGGAAGACATCCATGGCTTGATGAGCATGGTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAGATCGTCCTGATCTGACTGCCCCAGAAAGCTTACAGCTATACCTGGACACTAGAGTTGAACAACTAAAAATTGCTACAGAGCTCTCTCTCTGGCAGgtccgttccttatattttttaaccttttttatgccaagtgaatcatctttgctgtatgatcgtaaagctttgcttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT