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

gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaaagattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA

Basic information

species Oryza sativa
transcript LOC_Os01g51290.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
gtaagttttgatctgaaattattatctt-actacct-gtagttggtt-aacatcctcaccttaaa----aagattatg---aactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
||| | |   ||||||||||| |||||| ||| | |  |||||| || || | | ||| || | |    || ||| ||   || |  | |||||||| ||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||| ||||| || || |||||||||||||| || ||||||
gtatgcta-aatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
gtaagttttgatctgaaattattatcttactacct--gtagttggtt-aacatcctcaccttaa-----aaagattatg---aactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
||| | |   |||||||  || ||||||   |  |   ||| || || ||||||  || ||||      |||  |||||   || | || ||||||| ||||| |||||||| ||||||||||| |||||||| |||||||||||||| |||||||| || || || ||||||||||| ||||| || | ||||
gtacgctg-aatctgaacctactatctttacatttttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
---------gtaagttttgatctgaaattattatctt--actacctgtagttggttaacatcctcaccttaaaaagattat------gaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
          ||    ||| ||  ||  |||| | |    ||   ||   ||   || ||| |      | | |    |||       || |   | ||| ||||| || || || || |||||||||||||||||||| || ||||||||||| |||||||||||||| || || ||||||||| | || ||||| |||
attgcaatattaccacttggtcgaaacctattttttccagctggttgattttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
---------------------------------------------------------------------------------------------------------------gtaagttttgatctgaaattattatcttactacc-tgtagttggttaacatcc--tcaccttaaaaagattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
                                                                                                                 |   ||| ||  | |  ||   |   | | |  || | || ||  | ||         ||    | |||        |||  || || || ||||||||||| |||||||| || |||||||| || || |||||||| ||||||||||| || || ||||||||||| || || ||||| || 
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA09G07140.1 (Glycine max), 3'ss of exon 9
-----gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaa-------------agattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
      ||  ||||| |   ||| |||| |  | ||   | |  ||   ||  ||   | || | | |             | |||   ||  || || || ||||| ||||| || || |||||||| || |||||||| || ||||||||||| |||||||||||||| ||||||||||||||| | |||||||| |||
ctgaactattttttgtttcaaaactattgtaattctttgt-tgttttactattatttactccctgatatatatattctttcatatttgaaaaactattcagTTATGTGGCTCCGGAGTATGCAATGACGGGACATCTTCTTGTGAAGAGTGATGTTTACAGCTATGGTGTTGTCCTCCTTGAGCTTTTGACCGGAAGAAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G20590.1 (Glycine max), 3'ss of exon 9
-----------gtaagttttgatctgaaattattatcttactacctg-tagttggttaacatcctcaccttaaaaagattatgaactc-----tttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
           |    | |   |   ||  | |||| | |   | |   ||||  | || ||    ||   |   |  | ||  ||       |||  || ||  | ||||||||||| ||||||||||| |||||||| || ||||||||||| || || ||||| || || ||||||||||| || || ||||| || 
ttaagttgttaggtgatgtcatttaaaaggttttatttcatctcttaacagttcctcaagatgaaaactaaattcatctcattgacatgttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGATGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
-----gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaa-------------agattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
      ||| | ||| |   ||| |||| |  | ||   | |  ||   ||  || | | || | | |             | |||   ||  || || || ||||| || || || || ||||||||||| |||||||| || ||||| ||||| ||||| |||||||| ||||||||||||||| | || ||||| |||
ctgaactaattattgtttcaaaactattgtaattctttgt-tgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
--------gtaagttttgatctgaaattat-tatcttactacct----gtagttggttaacatcc--tcaccttaaaaagattatgaactcttttt--agGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
        || |  |||  | |  |   || ||  |||| |  |    | | ||  |  | ||         ||      ||||  | ||  ||||  || ||||| ||||||||||| ||||||||||| ||||| || || || |||||||| ||||||||||| || || ||||||||||| || |  ||||| || 
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA07G01210.1 (Glycine max), 3'ss of exon 10
--------gtaagttttgatctg---aaattattatcttactacctg-tagttggttaacatcctcaccttaaaaagattatgaactc-----tttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
         || ||  ||   ||   ||  | | || | |   | |   | ||  |||| ||    ||   |   |  | ||  ||       |||  || ||  | ||||||||||| ||||||||||| |||||||| || |||||||| || || || ||||| || || ||||||||||| || || ||||| || 
ttaagtggttaggtgatggcatgtaaaaggtttcatttcagctcttaacaattccttaaaatgaaaactgcattcatctcattgacatgttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGACGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
----------gtaagttttgatctgaaattattatctta--ctacctgtagttggttaacatcctcaccttaaaaagattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
            ||      ||| | |   | |   | |  ||   | |  |    |  |    | | |||| | | ||  |    |  |  ||||||||| || || |||||||||||||| ||||||||| | || ||||||||||| || || || || || || || || ||||| ||||| ||  |||||
gtaagataataaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaat-gttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 11
------------------gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaaagattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
                   ||  |||   ||     ||  | ||||  |   | |   |  |||     ||   ||   ||  |||||    ||   | |||||||| ||||| || || ||||||||||| |||||||| || ||||||||||| || |||||||| || ||||| |||||||| || || ||||| |||
atattcctgctttctttaatatttttaagtcccctgtttgtgtcttttttttttttaatt-ttatgtctctgttctcctaattattattttttcccatcagGTATGTGGCTCCAGAGTATGCAATGACTGGCCATCTTCTTGTGAAGAGTGATGTTTATAGCTATGGAGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
------------gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaaagattatgaactc-----tttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
            ||      |  | |    || |  |  |  ||    |   || || | |  ||||  |     |    || ||||      |||  || ||  | ||||| ||||| ||||||||||| |||||||| || || |||||||| ||||| |||||||| ||||| |||||||| || || ||||| || 
tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
-----gtaagttttgatctgaaattattatcttactacctgtagttgg----ttaacatcctcacct------taaaaagatta--tgaactctttt-tagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
      |   || |  | |     |||| | |   || || | | |||     || | |  | || |      |  |   | |   |||  |||  |  |||||||| || ||||||||||||||||| |||||||| || || ||||||||||| ||||| || || || || || || ||||| ||  | ||| |||||
ttctcttgtattctcgtttctt-ctattttttagatatctttggctggaccgctagcgttgttacttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S95_115V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaaagattatgaactct--ttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
                 |  | | || ||   |   | |||  | |  | | | || |      |     |  | |     |  |  | ||    |  ||||| ||||| ||||| ||||||||||| || |||||||| || ||||| || || ||||| ||||| || || || |||||||| ||  | ||| |||||
ttcttttacattggaccacatctagaactaccacattaatcagaatgtcaggacttagccttggtttctgcactgacctattggttgattcaaactgcagGTACGTTGCCCCTGAGTACGCAATGACAGGACATCTTCTTGTTAAGAGCGACGTTTACAGTTATGGAGTGGTACTTCTTGAGCTCCTCTCGGGACGGAAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
---gtaagttttgatctgaaattattatcttactacctgtagttggttaa--catcctcacctt--------aaaaagatta--tgaactctt--tttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
      |||| |||    |  || |    ||||    |  |   |   ||   ||  |   |||        |||  ||  |  ||||    |  |  |||||||| || |||||||| || ||||| || || ||||| |||||||| || || ||||||||||| || ||||| ||||| |||||| | || ||||  
accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S293_24V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcc--tcaccttaaaaagattatgaactctttt-tagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
                                             || |||    |||| | | |  |       |   |||| ||  |    ||    ||    | |  |||| ||    |  |    || ||||| || ||||||||||| ||||| || || || ||||| ||||| || || ||||||||||| || || || |||||||||||  | || ||||  
gtaggaactgcttttgtcatggtttttcagcacggagattaactcgtgagtgc-aatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaatacgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG

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|88735534|gb|CI759042.1|CI759042
EST:     ATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGG                         GTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGA
genomic: ATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGGgtaagttttg ... ctctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGA
EST: gi|58665758|gb|CK054444.1|CK054444
EST:     ATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGG                         GTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGA
genomic: ATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGGgtaagttttg ... ctctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGA
EST: gi|58678543|gb|CK067230.1|CK067230
EST:     ATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGG                         GTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGA
genomic: ATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGGgtaagttttg ... ctctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGA
EST: gi|313080020|gb|HO213340.1|HO213340
EST:     ATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGG                         GTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGA
genomic: ATAGGTGAGGGGAATGAGCATATTTCAACTCGTGTTATGGGAACTTTCGGgtaagttttg ... ctctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actacctgtagttggttaacatcctcaccttaaaaagattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
                     tcctcac  putative branch site (score: 2)
                                             ctcttttt  putative PPT
                             ttaaaaagattatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaaagattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA