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'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA

Basic information

species Oryza sativa
transcript LOC_Os04g52900.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
gtttgtttgtgaaaa-tacatgatatatcttctcgtttgcttttcttacatcata-----aatgttttttttggtactattgtc-cagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
|| || | ||||||| |||||| ||  |  |   | ||  |||| |  || | |      | ||   | |||  || |    |  ||||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||||| || || ||||||||||||||||||||||| |||||||||||
gtatgctagtgaaaaatacatgttagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA

upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 23
---gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcata-aatgttttttt--tggtacta-------------ttgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
    ||   || ||||   |  |  | ||  |  |   ||    |    | |||| | |||||  || |  |  || ||              | |  |||  ||||  |||||||||| ||||| |||||||| ||||||||||| || |||||||| || || || ||||| ||| | || ||||| ||| |||||||
tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA

upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 23
-------------------gtttgt-ttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtac-tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
                    ||  | || || |  ||  ||| ||||    |  ||   |  | | |    |  ||| ||    |        | |    |||  ||||  |||||||||| ||||| || ||||| ||||||||||| || |||||||| || || || ||||| ||| | || ||||| ||| |||||||
agaatattttaacttctgaattaatgttttgcaggtaattgaaatataaaat--ttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA

upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 23
gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
|||||| |||      | | |||||   |    || || |  |      | | |||   || || | ||          |||  | ||  |||| ||| | ||||| |||| ||| ||||||||||| || |||||||| || || |||||||| ||| |||||||||||||    |||||
gtttgtgtgtagtttaagacgatat---tgtaagtatgatcctgaattctgagaaacagttcttcttgt---------tagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA

upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: Vv10s0003g04460.t01 (Vitis vinifera), 3'ss of exon 5
gtttgtttgtgaaa--atacatgata-----tatcttctc--gtttgcttttctt-----------acatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
 |||    ||||||  | ||||||||      || |||       |  |||||||           ||   |||| | |  || |   |  |||  |  |||| ||||  |||||||||| |||||||| ||||||||||||||||| || || ||| | || ||  | || || ||||| || ||  |||| |||| |||
-tttcacggtgaaacaaaacatgataaaaatcattttcctcaacatatttttctttccgagaatatactgtataattctaattgtcatttttataatgtagGTACTGTGAGATTTAATCTTGATCCTTTCAATGAGCACAATGATGCTGACCTTTGGAAGGCTCTAAAGAGAGCACATCTCAAGGACTTCATTAGGATGAA

upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 23
-----------gtttgtttgtgaa-aatacatgatatatcttctcgtttgcttttctta-catcataaatgttttttttggtacta-ttgtcc-----agGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
           | |  |  || |  ||| ||  | || |    |  |    |||| |||      |   |||| || |    |  | ||||       |||  |||| ||||| ||||| |||||||| || |||||||||||||| || |||||||| ||  | || ||||| ||| | || ||||| || ||||||||
attactgataagatcctaagttatcaattcaatacattttagttaataaattttttttaatgaagtttgtgttattctaatgatcacttgtttcacatagGAACTGTGCGATTCAATCTTGATCCTTTCAACGAGCACAATGATGCTGACCTCTGGGAGGCTTTAGAGAGGGCACATTTGAAGGATGTTATCAGGAGGAA

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|33381540|gb|CF196883.1|CF196883
EST:     CCTACGAAAAGTACTAGGAATTATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|58691149|gb|CK079836.1|CK079836
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|58655688|gb|CK044368.1|CK044368
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|58690744|gb|CK079431.1|CK079431
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|29680004|gb|CB676279.1|CB676279
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|33793897|gb|CF322837.1|CF322837
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGA
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGA
EST: gi|58693939|gb|CK082626.1|CK082626
EST:     AGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: AGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|29671480|gb|CB667755.1|CB667755
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|58689770|gb|CK078457.1|CK078457
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|58588567|gb|CF986875.1|CF986875
EST:     CCTACGAAAAGTAGTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|58657519|gb|CK046199.1|CK046199
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|112786349|gb|EE590578.1|EE590578
EST:     CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: CCTACGAAAAGTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
EST: gi|84117316|gb|CD151083.1|CD151083
EST:     GTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAG                         GTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC
genomic: GTACTAGGAATAATACCACAGGCACCTGTCCTATTTTCAGgtttgtttgt ... tattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
               ttcttac  putative branch site (score: 2)
             ttttcttacatcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA