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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

Basic information

species Oryza sativa
transcript LOC_Os01g53680.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
||||   |||| |||||        | || | || ||    | |||| |||||||      || ||| ||    | ||   | ||||    ||| | ||            ||||  |||| |    | ||||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||| ||||| || || |||||||||||||| |||||||| |||||
gtaatcgtcttcttttt--------tacttggtgaac----gcagtgttagtttg------taatttata-gcatgtcaaggaatctg---atgaagtg------------cctgccatttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                            |||      |||  |     ||||||  | ||| |   |||      |   ||  |||  | | ||       | || |  | |||||||| || |||||||||||||| || ||||| |||||||| || ||||| |||||||| || || || || |||||  | ||||| |||||||| |||||
--------------------------------------------gtga-gacgtgagatctctttttttaactatatatttttattgaagaacaaaaaattg--acaccaataaaaaaattgtc-tcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 11
----gtaaagatcttgtttt-tatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
    |||||||        | ||| || |    |   || ||||| |   |||  ||| ||  |||   ||| | | || || ||  ||         ||||       ||  ||   | || |      || |||||||||| || |||||||| ||| ||||||||||||| || ||||| || ||||||||||| || || || |||||  ||||||| || ||||| || ||
gttcgtaaagacaaaaaactatatatttatacgtatgtgtacatgtg---tgcatgttcgat-taca--tttatgtgtgcat-tgcatactgaaaggaggaaatcaagcattgcatttttttttactatttgacagATCCAACGTATATGATCCGAGCAGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCCATGGCAGGTTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 11
gtaaagatcttgttt-ttatgttcaattctcgatgcacatgcg-gagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
           |||  ||| |   || | |  |   | | |   | ||||  ||||||  |  || ||| | |||| ||   |   |      | | |||   ||| |       | ||| |  |  || |||||||||| || |||||||| ||  ||||||||||||| || ||||| || ||||||||||| || || || |||||  ||||||| || ||||| || ||
-----------gttcgttaagacaaactatacaattatacgtatgtgtgcatgtttga--ttata-tttatgtatgcattgcatactgaaaggaggaaatcaagcattgcattttttttactatt--tgacagATCCAACGTATATGATCCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCGATGGCAGGTTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 10
---------------------------------------gtaaagatcttgttttta-tgttcaattctcgatgcacatgcggagtgctagtttgaagt--actactttttatatgtatctgagt-atctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                        ||   || |  |  ||| | ||  ||| |   | |  ||  | |  | |  ||  || |  |||     |||| |   | | | | |  |  ||    | ||    || |      |||||||     || |||||||||| |||||||| || ||||||||||||||||||||||||||||||||||| ||||| || || || |||||  | ||||| |||||||| || ||
gtcagtttctcttacagcattctcctcttcctttttgacctatttatttcttacttagtctttcatttttatttcggatttgaaaggttttttaaaatttgactgacaattatctcattttaattgagttatctgcctagtgggataagactttgttgttattgtatctgccagATCCAACTTACATGATTCGGGCAATTCCAAGCAATGCATCAGACAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 10
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgtt-------atttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                              |  || |  |  |  | ||  |  |    ||  |||| | | ||| |  || ||    ||   | ||  ||       ||||    ||  |||||| |||||||||||||| ||  ||||||| | |||||| || ||||| || ||||| || || || || |||||  ||||||| ||||||||||||||
----------------------------------------------gtgagctctat-tctttctactggtgcaaatgagagtgt-tacctgtataaagtaaatattctaaccaattgaaaaaaattttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtat-ctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                |    |         ||   | ||| ||  | | |  | |   |  ||||  |   |  |     |    | |||  |  |   |||| | | |   |||||||||| || ||||| || || |||||||||||||| || ||||| || ||||||||||| || || || |||||  ||||||| |||||||| || ||
-------------------------------gtttgtaaagattaaacttcatggaattataagtgtgcacacacacactgaaaagagcaatggctgaaagagtaatgccttctctttatgtttta---cagATCCAACTTATATGATTCGAGCTATTCCAAGCAATGCTTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 11
----------------gtaaagatcttgttttta---tgttcaattctcgatgca-catgcggagtgctagtttgaagtactactt-----tttatatgtatctgagtatctcc---ctatgga-atgttgcaataacagcctgttatttctaa---tggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                | |      |  |||||    | || | |||| | |    |||    | | |   ||| ||    |  ||     || | |  ||||| | | |  ||    |||  | ||  ||  ||||     |||| ||  |     || |||||||||| ||||||||||| ||||| | ||||||||||||||| ||||||||||| ||||| || || || |||||  | ||||| |||||||| || ||
gtcagtttctcttacagcattctcttcctttttgacctatttatttcttggtctttcatttttatttcggatttcaaaggttttttaaaatttgacaattatctaattttaaccaagttatctacatcgtgggataaggctttgttgttgttgtatctgccagATCCAACTTACATGATCCGGGCAATCCAAAGCAATGCATCAGATAATGTCTACTGTACACTTCTTGCTCAGAGTGCAGTCCATGGTGCAATGGCAGGGTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                                     |||  |     |||| |  ||||| |   |||      |   ||  |||  ||| |        |  |    | |||||||| || |||||||||||||| || ||||| |||||||| || ||||| |||||||| || || || || |||||  ||||||| |||||||| |||||
----------------------------------------------------gtgagctctcttttttaaactgtatatttttattaaagaacaaaaaattg--ataccgataaaaaaaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA07G01710.1 (Glycine max), 3'ss of exon 10
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                |  | ||  ||||   | |   |||  | || ||||     ||  |||    |||||  |   |   || | |  |          ||||   |   | || | ||    || |||||| |||||||||||||||||  ||||||| | |||||| || |||||  | ||||| || || || || |||||  ||||||| ||||||||||||||
---------------gtgagctctcttctttctactggtgca-aatggtagt-----gtgttac---ctatataaa---gtaaatgttctaac---------caattgaaattttttctgtc---cggtagATCCCACCTACATGATCCGTGCTGTTCCAAGTATTGCATCTGATAATGTACATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttt-tatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatg-gcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                 |    |   || |   ||||    | | ||  | | || |   |    |             ||| |    | |||   | | |  |||||  |   ||||||||||||| |||||||| || |||||||||||||| || ||||| || ||||||||||| || || || |||||  ||||||| |||||||| || ||
---------------------------------gtttgtaaagattaaaagttcatggaattatgtgtgtacacacactgaaaggagcaatggctgaaag----agtaatgccttctcttttctgttttacagATCCAACCTATATGATCCGAGCTATTCCAAGCAATGCCTCTGACAACGTGTACTGCACACTTCTTGCTCAAAGTGCAGTTCATGGAGCAATGGCAGGTTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                       |   |  | ||  ||     | |  || || | ||||| ||           ||  | | ||    |       || | | | |     ||||||||||||||||||| || ||  |||| |||||||||||||||||||| | |||||| ||  | || || || ||  ||||||| |  |||||||| ||
---------------------------------------gtatatagatatcttatg--agtttttcttttgtgtatgtggaacataatagataaagt-ttcttcttcttttttggtgtcttt-----cagATCCAACCTACATGATACGAGCTGTTCCGAGCAATGCATCAGACAATGTATGCTGCACGCTTTTAGCTCAAAGCGCGGTTCATGGAGTGATGGCTGGTTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttt--tatatgtatctgagtatctccctatggaatgttgcaataa--cagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                                         |||| | || |      || ||   | | |||||     || | |    ||    ||   |  |  |  ||||  |||||||||| |||||||| || ||  |||| |||||||| ||||||||||| || || ||||| ||||| || |||||  | || || ||||||||||||||
---------------------------------------------------------gtacaatttatatcccttgcattgcattctctccaccatgagtttcttgattgttcatttttcttgtcttaatttcagATCCAACATACATGATTCGAGCTGTTCCTAGCAATGCGTCAGACAATGTTTATTGTACACTTCTGGCTCAGAGTGCAGTGCACGGTGCAATGGCTGGATA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G56630.1 (Arabidopsis thaliana), 3'ss of exon 8
------gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatg-gcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
      || || | |||         |   |||||     |   | | ||    |   |   ||   |  |||     |||    |  |   |       ||||       | |         || || |||     ||||| || ||||||||||| ||  ||||||| ||||||||||||||||| ||||                                              
gtaagagttaaaaactttcaagatcatgagattcttatgccttttacagaaaatttcctcatagggtttatttcctcttgttgtagGATCATTTTAAGAAGAATAAGATGGTGATGA------ATCTCAAATACATTGATCCTACATACATGATCCGGGCTGTTCCAAGTAATGCATCAGACAATGTTTACT----------------------------------------------

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactact-ttttatatgtatctgagtatctccctatggaatgttgcaataacagcctg--ttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                                         ||||   | |  |      ||   |||    |   || || |  || | ||  |   ||  | |   |   |  ||||||| || ||||||||||| || ||||||  ||||||||| ||||| |||||||  || || || || || || ||  | ||||| ||||||||||| ||
---------------------------------------------------------gtacgtttgtcctccccaaattcaagtcgagctacatagattcatgaattagaaatatgactcaaaccatgtttcagATCCGACATACATGATCCGAGCTATTCCAGCCAATGCATCTGACAACGTCTACTCAACTCTCCTTGCCCAAAGCGCAGTCCATGGTGCAATGGCTGGCTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcc-tgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                      |  |       || ||   ||     | ||||| | |   |    || |  ||  | ||   |  | |   |||  |  |   |    | |||||||| || |||||||||||||| |||||| |||||||||| |||||||| ||||||||||| || || || |||||  ||||||| |||||||| || ||
-------------------------------------gtcagtgacttcagatttgtgtttgtttatttatttttccttttagatttggcttagtaacaatagattctaagctatcctgagttgtcttgcagATCCTACATACATGATCCGTGCTATTCCAGGCAATGCATCTGACAATGTGTACTGCACACTCCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGTTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaa-gtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaa-tggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                                  ||||| |   ||||  |||   || |||   || | ||    |  |  || |  ||  |    |||   ||| |   |  ||||||| || || |||||||||||  |||||||||||||||| ||||||||||| |||||||| || || || |||||  ||||||| |||||||| || ||
--------------------------------------------------gtttgtatacactatctttctaatatat---agaagctgggcaatggctggtctaaccaagtgctgcactttttgtctatcagATCCTACGTATATGATCCGTGCTGTTCCAAGCAATGCATCTGACAATGTCTATTGCACACTTCTTGCTCAAAGTGCTGTTCATGGAGCAATGGCAGGGTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgca-ataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
     |  | | |    |  |  ||   |         |      |||| | ||   || || || | |  ||| |  |   | |   | | |  |   ||| | || |   |     |  |      ||||||||||| |||||||| || ||  ||||||||||||| || ||||| || ||||||||  |||| || || || ||||| ||||| || ||||| || ||
---gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcaccacatgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaat------aacagcctgttatttc-taatg--gcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                      |||   |   ||  |  || ||  |  ||   |   |        | |  |||  | |        ||   |  ||    |   |  ||   |  || ||||| |       || ||   ||||  | || |   |||||||| || || ||||| || ||||||||||||||||| || |||||||||||||||||| ||||||| || || ||||| |||||||| ||||| || ||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggccacgtccatggtgatcttgcattcgataagactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaa---gtactactttttatatgtatctgagtatctccctatggaatgtt----gcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                     || |      ||| ||| ||   |  |||   ||  | ||      ||||    |  |  ||  | |     || ||||||  |||   | |   ||||||||||||| |||||||| || ||  | || || | |||||| || ||||| ||||||||  || ||||||| |||||||| ||||| || |||||||| | 
-----------------------------------gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacg--ctgaaagagcgctcaacacactaacagt-tgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ21599 (Selaginella moellendorffii), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                                                      |  ||  ||  || | |  ||      |  |    |  || | | | ||||       |||||||||| || |||||||| ||||| |  ||||| || || ||||||||||||||||| || || || |||||||| || || || ||||||||||| ||
---------------------------------------------------------------------gtcagtgcctacgtgtttttcttgccttttcttttctctcaacttttgatttt------cagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

upper sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ23976 (Selaginella moellendorffii), 3'ss of exon 11
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                                                      |  ||  ||  |  | |  ||         |    |  || | | | ||||       |||||||||| || |||||||| ||||| |  ||||| || || ||||||||||||||||| || || || |||||||| || || || ||||||||||| ||
---------------------------------------------------------------------gtcagtgcctacgagtttttcttgccttctcttttctctcaacttttgatttt------cagATCCAACGTATATGATCCGAGCAATCCGGAGCAACGCCTCGGACAATGTCTACTGCACTCTACTCGCTCACAGTGCGATCCACGGAGCAATGGCTGGCTA

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|112785640|gb|EE591113.1|EE591113
EST:     GATTACTGCAAGAACAAAAAGATGGAGATGACTATTAAGTATATAG                         ATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATTACTGCAAGAACAAAAAGATGGAGATGACTATTAAGTATATAGgtaaagatct ... ctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|89176257|gb|CI043278.1|CI043278
EST:     AGATGGAGATGACTATTAAGTATATAG                         ATCCTACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: AGATGGAGATGACTATTAAGTATATAGgtaaagatct ... ctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCT
EST: gi|66920247|gb|CX107095.1|CX107095
EST:     GATTACTGCAAGAACAAAAAGATGGAGATGACTATTAAGTATATAG                         ATCCAACCTACATGATCCGGTGCAATTCCAAGCAATGCATCAGACAATGTC
genomic: GATTACTGCAAGAACAAAAAGATGGAGATGACTATTAAGTATATAGgtaaagatct ... ctaatggcagATCCAACCTACATGATCC-GTGCAATTCCAAGCAATGCATCAGACAATGTC
EST: gi|89177192|gb|CI043695.1|CI043695
EST:     GATGGAGATGACTATTAAGTATATAG                         ATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCT
genomic: GATGGAGATGACTATTAAGTATATAGgtaaagatct ... ctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 8

GATTACTGCAAGAACAAAAAGATGGAGATGACTATTAAGTATATAGgtaaagatct ... ctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA
                                           ttctaat  putative branch site (score: 8)
                                       ttatttct  CT-rich tract
                                       ttatttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA