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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttaactgaaagatgtaccctctttcctgctatgaaccttcaactgatatttctcctatattgaagTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATG

Basic information

species Oryza sativa
transcript LOC_Os02g47220.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 7
gtattttaactgaaagatgtaccctctttc-----ctgctatgaaccttcaactgatatttctcctat---------attgaagTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATG
||||||||    |  | ||| |  | | ||     ||| | ||  | |||| |||||||||||  |||         ||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||||
gtattttagaccagtggtgttctttttatcattctctgttttgttctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 6
gtattttaactgaaagatgtaccctc----tttcctgctatgaaccttcaactgatatttctc-------ctatattgaagTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATG
||||||||    |  |||||    |     || |||| ||||  | ||||||||| ||||||         | | |||||||||||||||||||||||||| |||||||| ||||||||||| ||||||||  | |||||||| |||||||||||||||||||||||||||
gtattttagaccagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG

upper sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------gtattttaactgaaagatgtaccc-tctttcctgctatgaaccttcaactgatatttctcctatattga-------agTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATG
                                                        ||||| |   ||   | |   ||  || ||  ||    |   || ||| || ||   |  | ||  ||        |||||||||||    ||||||| ||||||||||||||||| |||||||||||  | ||||| ||   | | |  ||| |  | || || |||
gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattctttgtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG

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|58660884|gb|CK049564.1|CK049564
EST:     GAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGAGAGTAAAG                         TCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTAT
genomic: GAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGA-AGTAAAGgtattttaac ... tatattgaagTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTAT
EST: gi|88406810|gb|CI604004.1|CI604004
EST:     AGAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGAAGTAAAG                         TCTTTGCGGGGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATA
genomic: AGAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGAAGTAAAGgtattttaac ... tatattgaagTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtaccctctttcctgctatgaaccttcaactgatatttctcctatattgaagTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATG
                              aactgat  putative branch site (score: 3)
                                    tatttctcct  CT-rich tract
                                             tatattgaa  TA-rich tract