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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagctgttcatttgacgcctcacattttcgacacgcaagcagaacatacaatgcagtatattttttttcagacaggaaagattgttcattgcattgcattgttgtttgattttactgtcagGTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g55500.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55500.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G437859_T03 (Zea mays), 3'ss of exon 5
gtacgagctgttcatttgacgcctcacattttcgacacgcaagcagaacatacaatgcagtatattttttttcagacaggaaagattgttcattgcattgcattgttgtttgattttactgtcagGTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAG
             |     ||| |     |  |||| | ||    |      ||| |  |  |||  |      |||  ||   || | |   | |||   |||| ||| ||||  |    |||||||||||||||||||||| |||| || |||||| | || || ||||||||||| ||||||
-----------gtaccgctcgctttg---tcccgacccccatttcgtgttcccaacgtgg-gtatgct------gac--gaggaatggcttgct-catccgattgatgtctgataattgcatcagGTTGGGAGATGCGTTGAGATTGGCCTGCCAATGCTGATCCTCTTTGTCGTGCTGTCTCAG
















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|58599082|gb|CK009610.1|CK009610
EST:     CAGTGGTTGCATTGCTCGGGTTTGGCCTTTTCGAAAGAGGATTCCCTGTG                         GTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTCGTCGTG
genomic: CAGTGGTTGCATTGCTCGGGTTTGGCCTTTTCGAAAGAGGATTCCCTGTGgtacgagctg ... ttactgtcagGTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTG
EST: gi|88358900|gb|CI619404.1|CI619404
EST:     CAGTGGTTGCATTGCTCGGGTTTGGCCTTTTCGAAAGAGGATTCCCTGTG                         GTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTG
genomic: CAGTGGTTGCATTGCTCGGGTTTGGCCTTTTCGAAAGAGGATTCCCTGTGgtacgagctg ... ttactgtcagGTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagacaggaaagattgttcattgcattgcattgttgtttgattttactgtcagGTTGGGAGATGCGTTGAGGTTGGACTTCCAATGTTAATTCTGTTTGTCGTGCTTTCTCAG
                                     gtttgat  putative branch site (score: 5)
                                           ttttact  CT-rich tract
                                      tttgatttta  TA-rich tract