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

gtgcaaagtctatctatttctgttgttatactttcagcaatcgtccagtatcaggtgattaaccatatatgtaaaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G835235_T03 (Zea mays), 3'ss of exon 9
gtgcaaagtctatctatttctgttgttatactttcagcaatcgtccagtatcaggtgattaaccatatatgtaaa------atattt-agGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT
||| ||  | | ||||  | | || | ||  | | |  || |      || | | | | ||||    | | |  |      || ||| |||||||| | |||||| |||| ||||||||||||||||| |||||| |||| ||||||||||| || || || ||||||||||  
gtgtaat-tttttctacattttttataatgttctaaaaaaactgttgctaccggtttactaactgcctttttggatattttatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTG--

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G129482_T01 (Zea mays), 3'ss of exon 4
gtgcaaagtctatctatttctgttgttatactttcagcaatcgtccagtatcaggtgattaaccatatatgtaaa------atattt-agGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT
||| ||  | | ||||  | | || | ||  | | |  || |      ||   | | | |||     | | |  |      || ||| |||||||| | |||||| |||| ||||||||||||||||| |||||| |||| ||||||||||| || || || ||||||||||||
gtgtaat-tttttctacattttttataatgttctaaaaaaactgttgctactggtttactaattgcctttttggatattttatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G835235_T01 (Zea mays), 3'ss of exon 9
gtgcaaagtctatctatttctgttgttatactttcagcaatcgtccagtatcaggtgattaaccatatatgtaaa------atattt-agGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT
||| ||  | | ||||  | | || | ||  | | |  || |      || | | | | ||||    | | |  |      || ||| |||||||| | |||||| |||| ||||||||||||||||| |||||| |||| ||||||||||| || || || ||||||||||||
gtgtaat-tttttctacattttttataatgttctaaaaaaactgttgctaccggtttactaactgcctttttggatattttatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 9
gtgca-aagtctatctat-ttctgttgttatactttcagcaatcgtccagtatcaggtgattaacca--tatatgtaaaatat-----ttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT
||||  || ||| ||||  || ||||   ||||| | || || |    | | |   || | |||     | | |||| | | |     | |||||||||| |||||| |||| ||||||||||||||||| |||||| |||| ||||||||||| || || || ||||||||||||
gtgctcaaatctttctacattttgttacaatactctaagaaaactgttactgttgtgttactaatttactttttgtacattttatctttcagGTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT

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|33381492|gb|CF196835.1|CF196835
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58686155|gb|CK074842.1|CK074842
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58606572|gb|CK034605.1|CK034605
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTAGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58687307|gb|CK075994.1|CK075994
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58679602|gb|CK068289.1|CK068289
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58590369|gb|CF988677.1|CF988677
EST:     ACTATGCCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|218498670|gb|FG952679.1|FG952679
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58601780|gb|CK012308.1|CK012308
EST:     GTTCAAGTTTCCACAGATTAAAGCACACCCAGTGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCT
genomic: GTTCAAGTTTCCACAGATTAAAGCACACCCA-TGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCT
EST: gi|29618977|gb|CB623989.1|CB623989
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58602991|gb|CK013519.1|CK013519
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58672614|gb|CK061300.1|CK061300
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|38469291|gb|CF953422.1|CF953422
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|29677190|gb|CB673465.1|CB673465
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCT
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCT
EST: gi|86593838|gb|CI260067.1|CI260067
EST:     TACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: TACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|29677191|gb|CB673466.1|CB673466
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|218501528|gb|FG953636.1|FG953636
EST:     ACTAT-CCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|58682391|gb|CK071078.1|CK071078
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|66918477|gb|CX105325.1|CX105325
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|87007029|gb|CI275337.1|CI275337
EST:     AAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
genomic: AAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTG
EST: gi|2317500|gb|C22554.1|C22554
EST:     ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAG                         GTATTCCATAAAAGGTTGGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCT
genomic: ACTATACCGAGTTCAAGTTTCCACAGATTAAAGCACACCCATGGCACAAGgtgcaaagtc ... aaatatttagGTATTCCATAAAAGGTTG-CCTCCAGAAGCTGTTGATCTTGTCTCTAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttcagcaatcgtccagtatcaggtgattaaccatatatgtaaaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT
                            gattaac  putative branch site (score: 2)
                           tgattaaccatatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaaagtctatctatttctgttgttatactttcagcaatcgtccagtatcaggtgattaaccatatatgtaaaatatttagGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG