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

...gctatttgtctgtttattttacaactcattcttcacattctctgattgaaaccaaatgatcattacaatttgcagcaagtctaaattagttcttttgcagAATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCATAACATATGTAATGGTTGACGGTTGGACTGGTGTAGCTGGTGAAATATTG

Basic information

species Oryza sativa
transcript LOC_Os05g51630.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51630.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G456000_T01 (Zea mays), 3'ss of exon 9
gctatttgtctgtttattttacaactcattctt--cacattctctgattgaaacca--aatgatcattacaatttgcagcaagtctaaattagttcttt-tgcagAATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCATAACATATGTAATGGTTGACGGTTGGACTGGTGTAGCTGGTGAAATATTG
     | || | | | | | | ||   |||| |  || ||||||| | |||||  |  |||| |  | |  |||    |   |||||||||  || ||| ||||| ||||| || | ||| ||||   |||| ||||||| |||||||||||||||||||||||| |||||||| |||||||||||  |||||||||||||||||
-----tggtatatgtttctgataatctattccttgcatattctcttaatgaaattataaatggtagtcatgattgctggagtgtctaaattgcttgtttctgcagCATACCAAGGATCATTGGTGACTCCATCCCAATGAAGGCGACTTTTTTCATAACATATGTGATGGTTGATGGTTGGACTGGAATAGCTGGTGAAATATTG
















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|29678912|gb|CB675187.1|CB675187
EST:     GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGA                         AATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
genomic: GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGAgtaagtactc ... tcttttgcagAATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
EST: gi|218494751|gb|FG955894.1|FG955894
EST:     GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGA                         AATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
genomic: GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGAgtaagtactc ... tcttttgcagAATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
EST: gi|58693113|gb|CK081800.1|CK081800
EST:     GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGA                         AATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
genomic: GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGAgtaagtactc ... tcttttgcagAATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
EST: gi|58686140|gb|CK074827.1|CK074827
EST:     GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGA                         AATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
genomic: GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGAgtaagtactc ... tcttttgcagAATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
EST: gi|218492846|gb|FG945413.1|FG945413
EST:     GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGA                         AATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT
genomic: GGATCTGCTTTAGATCAGCTTAAGGCATACATTCATCAGTCGGCAAATGAgtaagtactc ... tcttttgcagAATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaaccaaatgatcattacaatttgcagcaagtctaaattagttcttttgcagAATACCGAGAACCATCGGTGTAGCCATTCCAATGAGGGCGACTTTTTTCATAACATATGTAATGGTTGACGGTTGGACTGGTGTAGCTGGTGAAATATTG
                                 gtctaaa  putative branch site (score: 3)
                                            ttcttttgc  putative PPT
                                    taaattagttctttt  TA-rich tract