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'   
14  
 5'  3'   
15  
 5'  3'   
16  
 5'  3'   
17  
 5'  3'   
18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag

Basic information

species Oryza sativa
transcript LOC_Os11g33240.3
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 4
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag
||||| ||||||||||| |||||||||||||||||||||||| ||||||||||||||||| |||||||||| ||||||||||| | || || | || | ||| | ||| |||| || | | ||| |||| || ||| || ||| ||| ||| | | |||| | ||||
GTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgttta----tgcttgtgatttagtctagatagcaa-tttagtcctctttttact------tagcaaatctagttctgagtgagcact-aatgtttggaac--actaactgtgcag

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag
||||| ||||| ||||| |||||||||||||||||||||||| ||||||||||||||||| |||||||||| ||||||||||| || || | |||||| | | |||||| | || || | |||||||| | ||| ||| ||| ||| | || |||| | ||||
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgttta--tgctttg------tcatttag-attccaatttagtgatgtttttat--ttacttagtaaataaagttctgaatgagcactc---atgtctggaacactaactgtgcag

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 17
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaac-gagtacttaataaaagcggccat-ctaattacgcag
||||| ||||||||||| |||||||| |||||||||||| | ||||||||||||||||| |||||||| | |||||||||| | | ||| ||| | || ||| | || | || || || | | | || || ||| ||| | | | | | | | || | ||||
GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcag

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA15G42300.1 (Glycine max), 5'ss of exon 18
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgt--ttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag
|| ||||| |||||||| ||||||||||| ||||||||||| || |||||| ||| ||| || |||| | ||||| |||| | || | | || || | ||| || ||| | || | | || ||| | | | | || |||| | | || ||
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacctgttccacttg--aaatagttttcattttgcaattatttttttagggtgaatttcatcta--atgatctattaacatc-gtggacag------------

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgt--ttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag
|| ||||| |||||||||||||||||||||||||||||||| || |||||| | | ||| || |||| | ||||| |||| | || || | || || | ||| || ||| | || | | || ||| || | | | || |||||| | || ||
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttg--aaatagttttcattttgcaattattttttag-ggtgaatctaatcta--atgatctattaatatt-gtggacag------------

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtt-tacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag
|| || ||||| ||||| |||||||||||||||||||| || |||||||||||| ||| || | ||||| |||| | || | | || || | | | | | ||| | | || || || |||| | || || | |
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagta--tcattgagc---cttaggatagcactca-aatataata-tctgtgcgttttatag------------------------------------

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 18
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatt-taatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag
|| |||||||||||||| ||||| |||||||||||||| || |||||||||| ||||| ||| ||||| ||||| || || || | | || | | || | | ||| | || | || | | | | || | |||| || | || | |
GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACGgtaaagagttctctctca--caatcattataattggagatttcttaatttggctatttaatagtatcttgggtagatggtaaaa--atcctttaacaattgatcccttgcag--------

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 5'ss of exon 16
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatgga-atagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag
|| |||||||||||||| ||||| |||||||| |||||||| |||| | |||| ||| | ||| || | ||| ||| || || || | | || | | | | | | || || | || || | | | || || || | |
GTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAAgtgagcagtccttcccttgtaaactattcaattattccactcaggtttagggaatctgttgcctgcaccaagtgggtggacttatgttgatttgatgaatgtgcag--------------

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|163929405|gb|EG713830.1|EG713830
EST:     GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
EST: gi|86504183|gb|CI146816.1|CI146816
EST:     GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
EST: gi|89175851|gb|CI042872.1|CI042872
EST:     GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
EST: gi|88266492|gb|CI377394.1|CI377394
EST:     TATCTGAAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: TATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
EST: gi|88255207|gb|CI354031.1|CI354031
EST:     ATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: ATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
EST: gi|86500499|gb|CI143132.1|CI143132
EST:     GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
EST: gi|88247059|gb|CI246908.1|CI246908
EST:     TGCTGAACCACTTTGGATTATCTGGAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: TGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
EST: gi|89186485|gb|CI048157.1|CI048157
EST:     GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
EST: gi|86480028|gb|CI122661.1|CI122661
EST:     GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG                         GTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttac ... aattacgcagGTATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag

- - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC