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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGAAGCTCAACCTTCCAGTCCTTCCTACAACCACAATTGGTTCATTCCCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaacagtccacatcaacgcttcaccgttttcccccttttttttgtctatattgctaattacaattcctgctacag

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G149751_T06 (Zea mays), 5'ss of exon 7
AGAAGAAGCTCAACCTTCCAGTCCTTCCTACAACCACAATTGGTTCATTCCCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaacagtccacatcaacgcttcaccgttttcccccttttttttgtctatattgctaattacaattcctgctacag
|||||||||| ||||| ||  ||||||| || || ||||| ||||| |||||||| || || ||||||||||| |||||||||||||||||||| |||||||| ||     |     | ||  | |  |     |   |  | |||| |    | ||  || |    ||||      |||
AGAAGAAGCTTAACCTCCCCATCCTTCCCACCACTACAATCGGTTCGTTCCCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtcat-----ttaatacctagcttcacttgtctgtattttggctggttttcttattggagattcacatcgcag
















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|300215517|gb|HO088143.1|HO088143
EST:     CCACAGAATGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|218492493|gb|FG951515.1|FG951515
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|300216253|gb|HO088038.1|HO088038
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|11863315|gb|AU065792.2|AU065792
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|29637650|gb|CB642659.1|CB642659
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|218478602|gb|FG965538.1|FG965538
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGT-CAAGGCTAAAAA                         GATCTCTGAGGAT-AGTACGTCAGTGCCATCAAGGAGG-AATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|58613186|gb|CK040898.1|CK040898
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|571921|gb|D41432.1|D41432
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|218483058|gb|FG951439.1|FG951439
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|88724067|gb|CI749077.1|CI749077
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|4968885|gb|AU065789.1|AU065789
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTNCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|571693|gb|D41204.1|D41204
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTNCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|29615679|gb|CB620691.1|CB620691
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCAT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCAT
EST: gi|88718273|gb|CI741362.1|CI741362
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|570079|gb|D40928.1|D40928
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|88729113|gb|CI752623.1|CI752623
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|58688902|gb|CK077589.1|CK077589
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|33800724|gb|CF326232.1|CF326232
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
EST: gi|58661898|gb|CK050578.1|CK050578
EST:     CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAA                         GATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT
genomic: CCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaaca ... cctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGAAGCTCAACCTTCCAGTCCTTCCTACAACCACAATTGGTTCATTCCCACAGACTGTGGAGCTCAGGAGAGTCCGCCGTGAGTACAAGGCTAAAAAgtgcgtaacagtccacatcaacgcttcaccgttttcccccttttttttgtctatattgctaattacaattcctgctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA