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'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtacttgatccttaccatattcatgttaaatagaagcagttggtaatagtgggtgttctctaaggaactaggtgcgcactgtctatatagctgaactgtaatgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G081322_T01 (Zea mays), 5'ss of exon 13
GGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtacttgatccttaccatattcatgttaaatagaagcagttggtaatag-tgggtgtt---ctctaaggaactaggtgcgcactgtctatatagctgaactgtaatgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcag
||||||||||||||||| ||||| |||||||||||| | ||  |||||||||| ||||| ||||| |||||||||| ||  |   | |  || | ||||| | |  ||   ||||  | |||  || ||| |   ||  || |||||   || |  |  |||||| |  ||||   |  | |  ||  | | | |   | | || |    | ||||||||  | ||  |||||
GGTCGTATTTATCAAGGAAAAGAGCCACCACAATTTGTGGCTATTTTCCAGCCAATGGTTATTCTTAAGgtatggtgctc-actgtgattatgt-catgt-atagggagttagttaatgataaatgtgtgctggtctgcaaagaactcattg-gagcattctatagaaatgaaaaatgttttgtaacgttactcc---cgaaattacggcaatgtatttgtaaaatcatgcag

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G323479_T01 (Zea mays), 5'ss of exon 18
GGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtacttgatccttaccatattcatgttaaatagaagcagttggtaatagtggg-tgttctctaaggaacta-----ggtgcgcactg---tctatatagctgaactgtaatgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcag
||||| ||||||||||| |||||||||||||||||| |||| ||||||||||| ||||| ||||| |||||||| | || | |  | |  || | |||||  | |   ||    || |||  ||| | || |||  || |||||      || ||   |||   |||||  |  ||||   |  | |  ||  | | | || | | || |||   | ||||||||  | ||  |||||
GGTCGCATTTATCAAGGAAAAGAACCACCACAATTTGTTGCTCTTTTCCAGCCAATGGTTATTCTTAAGgtatgatgctcgctg-tgattatgt-catgtatagtg--agttaatgataaatgtgtgctggtctgcaaagaactcatattggagcattctgcattctatggaaatgaaaaatgttttgtaacgttactccagaaattaccag---aatgtatttgataaatcatgcag

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA19G32010.1 (Glycine max), 5'ss of exon 13
GGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtacttgatccttacca-tattcatgttaaatagaagcagttggtaatagtgggtgttctctaaggaactaggtgcgcactgtctatatagctgaactgtaatgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcag
||||| || | | | || ||||| |||||||| ||||||||||||||||| || |||||  | || |||||||  |     |     |    ||||  | ||||     ||   |||     |||   |      || |  ||  |    |   ||||||  |                                                                   
GGTCGCATATTTGATGGTAAAGAGCCACCACAGTTTATTGCCCTTTTCCATCCAATGGTGGTCCTCAAGgtatcatttgcaaaatccaatgctatttttattaacatatagagattgtctgaagttaat------taggttacctgacttg---tgtctaactcag----------------------------------------------------------------

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|58670584|gb|CK059270.1|CK059270
EST:     AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG                         GGTGGAATCAGCTCTGGATACCAGAAATGTGTAGAAGAAAAGGGCTTGAAG
genomic: AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
EST: gi|88692350|gb|CI735925.1|CI735925
EST:     AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG                         GGTGGAATCAGNTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
genomic: AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
EST: gi|12404685|gb|AU166286.1|AU166286
EST:     GGTCATTCTAAAG                         GGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
genomic: GGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
EST: gi|426363|gb|D22226.1|D22226
EST:     GGTCATTCTAAAG                         GGNGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
genomic: GGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
EST: gi|88569524|gb|CI660699.1|CI660699
EST:     AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAG                         GGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG
genomic: AAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtact ... tattgtgcagGGTGGAATCAGCTCTGGATACCAGAAATTTGTAGAAGAAAAGGGCTTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCGTATTTATCAAGGGAAAGAACCACCACAATTTATTGCCCTTTTCCAGCCCATGGTCATTCTAAAGgtatggtacttgatccttaccatattcatgttaaatagaagcagttggtaatagtgggtgttctctaaggaactaggtgcgcactgtctatatagctgaactgtaatgtccaatctcaattcaaacaatatcagttaagtgtatttggcatattgtgcag

- - - - - - - - -  AAGAAC