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

gtaagtcttctgcaatgtcaacatcaaggttttttgtgcaagtaattcacatttatgcttctgatcataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCTCCCACAG

Basic information

species Oryza sativa
transcript LOC_Os02g03580.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G153144_T01 (Zea mays), 3'ss of exon 7
gtaagtcttctgcaatgtcaaca--------tcaaggttttttgtg--caagtaattcacatttatgcttctgatcataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCTCCCACAG
|| |||| | | ||| |||||||        | || ||   |||    |||| |||| |   |||   ||||| | | |||||||||||||| ||||| |||||||||||||| |||||||||||| ||||||||||| |||||
gtgagtcatttccaa-gtcaacagttcattataaaagtcaattggagtcaagaaattgag--ttagatttctggtaacaatttcagGGAAAAGTGAGCCTGGCAGAACATCTGCTCCATCTGCCAATGGGATTACCTCGCACAG

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G387310_T01 (Zea mays), 3'ss of exon 6
gtaagtcttctgcaatgtcaaca--------tcaaggttttttgt-gcaagtaattcacatttatgcttctgatcataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCTCCCACAG------------------------------------------
||  ||||| | ||| || ||||        |||| ||   |||  ||||| || | | | |||  |||||| | | ||||||||||||||  |||| ||||||||| |||| |||||| ||||||||||||||||| ||||                                           
gtgcgtctttttcaaggtgaacagctcattatcaaagtcagttggagcaaggaaatta-aattagacttctggtaacaatttcagGGAAAAGCGAGCCTGGCAGAACGTCTGCTCCATCCGCCAACGGGATTACCTCGCACAAGTTTTTATTTCTTGGTGTGCAAGTTACAGATTTTCTGTAATT

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G164848_T01 (Zea mays), 3'ss of exon 5
gtaagtcttctgcaatgtcaaca--------tcaaggttttttgt-gcaagtaattcacatttatgcttctgatcataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCTCCCACAG
||  ||||| | ||| || ||||        |||| ||   |||  ||||| || | | | |||  |||||| | | ||||||||||||||  |||| ||||||||| |||| |||||| ||||||||||||||||| ||| |
gtgtgtcttttccaaggtgaacaggtcattatcaaagtcagttggagcaaggaaatta-aattagacttctggtaacaatttcagGGAAAAGCGAGCCTGGCAGAACGTCTGCTCCATCCGCCAACGGGATTACCTCGCACCG

upper sequence: LOC_Os02g03580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G019106_T01 (Zea mays), 3'ss of exon 7
gtaagtcttctgcaatgtcaaca--------tcaaggttttttgt-gcaagtaattcacatttatgcttctgatcataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCTCCCACAG
||  ||||| | ||| || ||||        |||| ||   |||  ||||| |  | | | |||  |||||| | | ||||||||||||||  |||| ||||||||| |||| |||||| ||||||||||||||||| |||||
gtgcgtcttttccaaggtgaacagctcattatcaaagtcagttggagcaaggagatta-aattagacttctggtaacaatttcagGGAAAAGCGAGCCTGGCAGAACGTCTGCTCCATCCGCCAACGGGATTACCTCGCACAG

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|29670500|gb|CB666775.1|CB666775
EST:     GGAACTGCACCAGGTGCTTCAGAAATTAACG                         GGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCT
genomic: GGAACTGCACCAGGTGCTTCAGAAATTAACGgtaagtcttc ... ataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCT
EST: gi|32948093|gb|BP184665.1|BP184665
EST:     GGAACTGCACCAGGTGCTTCAGAAATTAACG                         GGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCT
genomic: GGAACTGCACCAGGTGCTTCAGAAATTAACGgtaagtcttc ... ataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCT
EST: gi|32948307|gb|BP184879.1|BP184879
EST:     GGAACTGCACCAGGTGCTTCAGAAATTAACG                         GGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCT
genomic: GGAACTGCACCAGGTGCTTCAGAAATTAACGgtaagtcttc ... ataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcaaggttttttgtgcaagtaattcacatttatgcttctgatcataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCTCCCACAG
                                     ttctgat  putative branch site (score: 3)
                     taattcacatttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttctgcaatgtcaacatcaaggttttttgtgcaagtaattcacatttatgcttctgatcataatttcagGGAAAAATGAGCTTGGCAGAACATCTGGTCCATCTGCCAACGGGATTACCTCCCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT