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

gtaacatctgatttagtttagtggaatattattctatgtagtttcccccttttcttttagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG

Basic information

species Oryza sativa
transcript LOC_Os01g19150.5
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G075992_T01 (Zea mays), 3'ss of exon 5
gtaacatctgatttagtttagtggaatattattctatgtagtttcccccttttcttttagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG----
|||| |  ||| ||  || | | ||| |||   ||   ||||| | |  ||| |  ||  ||||||   ||| |||| |    ||| ||||||| || |||||||||||| |||| ||||| || |  |||||||| |||||||| || |||||||| || ||||||||||||||||||||||||||     
gtaatag-tgacttctttcaattgaagatttagcttgctagttacaca-tttccagttgactcatg---gaggcttatt---tttctttcagGTTCTAGGTACTCCAACACGGGATGAAATTAAGCGCATGAATCCAAACTACACCGAATTTAAGTTTCCGCAAATCAAAGCTCACCCATGGCACAAAGTAA

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 9
---------gtaacatctgatttagtttagtggaatattattctatgtagtttcccccttttcttttagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
          |    ||| |  ||| ||  | | | || ||||    ||||| ||   || ||||||    | |         |   ||     |||||||||  | ||||| ||||||||||||||||||||    |||||||| || || || ||||  || || || ||||| |||||||||||||||||||||
tgtgattgcattttctcttaactagcttgtttgtagat-attcataatagttcccttgttatcttttcatacttctgaagaggtctgtgattcacattcagGTTTTAGGTACCCCAACAAGGGAAGAAATCAAGTGCATGAATCCTAATTATACCGAGTCCAAATTTCCACAAATTAAAGCTCACCCATGGCACAAG

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 9
-------gtaacatctgatttagtttagtggaa--tattattctatgtagtttcccccttttcttttagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
        ||| |      ||  |||| |      | ||     ||  |||  ||   || ||||| ||  | || |      ||   |     ||| |||||  | || || || |||||||||||||||||   ||||||||| || ||||| ||||| || || || ||||| |||||||| |||||||| |||
atccataataatagtccccttgttttatttttcccttttgcctcattcagtg-ccgtgttatctttgagtacttgtaaagagatttgggattcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTACACCGAGTTCAAATTTCCACAAATTAAAGCTCATCCATGGCATAAG

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 9
----gtaacatctgatttagtttagtggaatattattcta---tgtagtttcccccttttcttttagc-tcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
    |     ||||   | | |   |   || || ||      | |||| |||  |  || ||   |  |  |  |  | | || ||    | ||| |||||  |||| || |||||||| || ||||| ||    |||||||| || ||||| || ||||| ||||| ||||| ||||| |||||||||||||||
tggtgctgagtctgcagttgctcctttccatcttgtttgtgattttagtatccatcccttattaatgtgttttctacaatattttcttatttgcatgcagGTTTTGGGCACCCCAACAAGAGAGGAAATTAAGTGCATGAATCCCAATTACACAGAATTTAAATTCCCACAAATTAAAGCCCACCCATGGCACAAG

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------------------------------------------------------------------gtaacatctgat-ttagtttagtggaatattattctatgtagtttcccccttttcttt-tagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
                                                                                                        ||   | ||| |  | | |  |||  || ||| | ||||   |  |     |   | | |||  | |   ||    |    ||  |    | ||||  |||| || || ||| | || || || ||    ||||||||||||||||| ||||| ||||| || ||||| || ||||| || |||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagt-tatgacttcgctagaatggatatgtaggacttatgggtagttgg--gtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------gtaacatctgatttagtttagtggaatattattcta---tgtagtttcccccttttcttttagc----tcatgcaggagacttactgtacttca-------tt------cagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
           |  |     | | | || | |  |  |    | ||    ||  | ||    || ||     ||     | |||| |  || |   |||  || |       ||      |||||  |||| || || ||  | || || |||||    ||||||||||||||||| ||||| ||||| || |||||||| ||||||||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgtggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------gtaacatctgatttagtt--tagtggaatattatt-ctatgtagtttcccccttttcttttagctcatgcaggagacttact-gtacttcatt--cagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
                              | |    ||   || ||  | |  |  | | | |  |  |  | |       |    |  ||     | | |  | | |   ||||||   |  |||||  |||| || || ||  | || || || ||    ||||||||||||||||| ||||| ||||| || |||||||| |||||||| |||||||| 
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------gtaacatctgatttagtttagtggaatattattctatgtagtttcccccttttcttttagctcatgcaggagacttactgtacttcatt--cagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
                                          | ||||  || |     |||  | |   | |  |||  ||   | | ||   |  |   |||  |  |||     ||       |  |||||  |||| || || ||  | || || |||||    ||||||||||||||||| ||||| ||||| || |||||||| || ||||| |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtg-gtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------------------------------------------------------------------gtaacatctgatttagtttagtggaatattatt-ctatg-tagtttcccccttttcttttag--ctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
                                                                                                  |   | ||| | | |||   | |  |  | || |  || |||        |  |  | |||  || ||| || || |  |  ||  |     |||||  | || || || ||| | || || || ||    ||||||||||||||||| ||||| ||||| || ||||| || |||||||| |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatg-agtaggcggatggtgatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtaacatctgatttagttta-gtggaatattattctatgtagtttccccctttt-cttttagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
               ||     || | | ||  ||| | |  | |     |||| |   | |||| |||   |||||| || |      | |||||  | |||||||| ||  | || |||||||||   |||||||| |||||||| |||||||||||||| || || ||||| || || |||||||||
---------------gtacgcatgcattcttgctcttttttttctgttttttttgcgagtcgctcttgctcaagacttgcttt------tgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtaacatctgatttagttta-gtggaatattattctatgtagtttcccccttttcttttagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
               ||     || | | ||  ||| |    |||  |  ||| |   | |||| |||   |||||| || |      | |||||  | |||||||| ||  |||| |||||||||   |||||||| |||||||| |||||||||||||| || || ||||| || || |||||||||
---------------gtacgcatgcattcttgctctct----tttttctttttgcgagtcgctcttgctcaagacttgcttt------tgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

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|29628248|gb|CB633259.1|CB633259
EST:     CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAG                         GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
genomic: CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
EST: gi|33683226|gb|CF311465.1|CF311465
EST:     CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAG                         GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
genomic: CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
EST: gi|29668828|gb|CB665103.1|CB665103
EST:     CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAG                         GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
genomic: CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
EST: gi|8856575|gb|AU093893.1|AU093893
EST:     TGAAATTATCAAG                         GTACTGGGTACTCCCAACAA-GGNAGAATTCAAACATATGAATCGGAACTA
genomic: TGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACT-CCAACAAGGGAAGAAATCAAACATATGAATCCGAACTA
EST: gi|58675098|gb|CK063785.1|CK063785
EST:     GTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAG                         GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
genomic: GTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
EST: gi|29666992|gb|CB663267.1|CB663267
EST:     CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAG                         GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
genomic: CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
EST: gi|29628183|gb|CB633194.1|CB633194
EST:     CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAG                         GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
genomic: CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
EST: gi|29666642|gb|CB662917.1|CB662917
EST:     CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAG                         GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
genomic: CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
EST: gi|218502361|gb|FG956952.1|FG956952
EST:     CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAG                         GTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC
genomic: CTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctg ... cttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtttcccccttttcttttagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG
                                  gacttac  putative branch site (score: 2)
                                             cttcattc  putative PPT
            ttttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatctgatttagtttagtggaatattattctatgtagtttcccccttttcttttagctcatgcaggagacttactgtacttcattcagGTACTGGGTACTCCAACAAGGGAAGAAATCAAACATATGAATCCGAACTACACTGAGTTTAAGTTCCCCCAAATCAAAGCTCACCCATGGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA