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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC

Basic information

species Oryza sativa
transcript LOC_Os03g40180.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G024354_T01 (Zea mays), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctct-ctcctgatccgtcctccgtcgttttgctgt-gcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
                                     |   | | | ||   |   || | ||     | || | | | |  ||  ||     | || |    || || |||| |||||||||||||||||||| |||||||||||||||||||||||||||||| | ||||||||||||||||| |||||||||||||||||||||||| |
--------------------------------gtgagcaaatgttctgtggtctctccgtgcaggcgaacctttgcgcgtcgtctctctctgatagtctgttcgtcgcgcagGGGCGTACAAGTACGTGTCGGAACTATGGAGGAGGAAGCAGTCGGACGTGATGCGCTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G034794_T02 (Zea mays), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcct-ccgtcgttttgctgtg-cacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
                     |    |   | |   |  ||      |  ||   ||  | | | | | |   |||     |  ||| |  | |  | | |||||| ||||||||||||||||||||| |||||||||||| ||||||||||||| || |||||| ||||||||||||||||||| ||||||||||||||||||||||||||
---------------------gtgagctctcgtatttaccgctgatggcctct--ccgattcgcatgcgtgggtcttaccgtgtgtcgtatcattttgtcgctgtggcacagGTGCGTACAAGTACGTCTCGGAGCTATGGCGGAGGAAGCAGTCCGATGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G180724_T01 (Zea mays), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
                  |     || |  |  ||    |||||||  ||     | | | ||      | |      || | | || |   ||| | ||    || |||| ||||||||||| || |||||| |||||||||||||||| || ||||||||| ||||||||||||||||||| ||||||||||||||||||||||||||
------------------gtgagttctcggctacaaggccgtctccgatt-----cgcatgcatgggtttttacggtatgttgcatcgtttctcgctgtg----gcgcagGGGCGTACAAGTATGTCTCGGAGTTATGGAGGAGGAAGCAATCCGACGTGATGCGGTTCGTGCAGCGCGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G084757_T01 (Zea mays), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtg-cacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
               |      | |  | | | | ||   | |  |    ||| |  |   ||  |      || | | |     | | ||||  | | |||||| | |||| |||||||||||||| |||||| ||||||| |||||||| || ||||||||| ||||||| || |||||||| || |||||||||||||||||||||||
---------------gtgagttcttggccctaccgctgatgccctc----tccgattcg--catgtgtggggctttacggtatgttgcaccgtt-tctcgctgtggcgcagGGGCGTACAAGTACGTCTCGGAGTTATGGAGAAGGAAGCAATCCGACGTGATGCGGTTCGTTCAACGCGTGCGCTGTTGGGAGTACAGGCAGCAGCCGGC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G15230.1 (Glycine max), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtc--tccagtttcccacccctccacctccatctctctcctga--tccgtcctccgtcgttttgctgtgc------acagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
                     ||     || || | |   |    |  || || | | |    ||  |   |   |||  |||  |  | | |   | || ||| | |        | |||||| |||||||| || |||||||||||| | | ||||||||| || || ||||| ||| ||||||| ||| |||||||||||||  | ||||| ||  |
--------------------tgctgatttctattagttatgctggttgagctttctatcatagcatttttgttattctagtgaaattaggcattatttgtgttggtttatgttgcaatagGTGCCTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTATCGCCAGCAACCTTC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G41620.1 (Glycine max), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
            |    |      |   ||        |  | |   ||  ||         |     ||   |     |    ||      | || |   ||   | |||||| |||||||| || || ||||||||| | | ||||||||| || || ||| | ||| ||||||| ||| ||||||||||||| |||||||| ||  |
---------atatatagcttttggttattctgatggaattatgtgtggta-cctgtgttggaagtgtaattgataaaacgtgttgtttatgttggtgtgattggcaatagGTGCCTACAAGTATGTTTCAGAGCTATGGCGCAAGAAGCAGTCTGATGTCATGCGCTTCTTGCAGCGGGTGAGGTGCTGGGAGTATAGGCAGCAACCTTC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G04870.1 (Glycine max), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtc-ctccgtcgttttgctgtgca-cagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
    ||   || | |   ||    |  ||         ||   |  | ||   ||    |     |     |   |    ||   |   |   | |   |    ||||  |||||| |||||||| || |||||||||||| | | ||||||||| || || ||||| ||| ||||||| ||| |||||||||||||| | ||||| ||  |
----gcctttctttcatagcatttttgctat-------tcaagtgaaattaggcattgttt-gttttggaatgagtgaaaattgattattttattggaatatgttgcaatagGTGCTTACAAGTATGTTTCGGAGCTATGGCGCAAGAAGCAGTCTGATGTTATGAGATTCTTGCAGCGGGTGAGGTGCTGGGAGTACCGCCAGCAACCTTC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G17390.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
    |    |    |        ||| |||      | |||| ||   | |      | |     || |    |    | |    |     ||  ||||  ||   |||||||||||||| |||||||||||||||||||||| |||||||||||| |||||||||||  | ||| | ||  |||| ||||||||  | ||||||||  |
----gtatgtttctcactattatctctctct-cagatgtcgtttc---tgtattgttcattagattctagaagttaattaagg-atgaaatgtgatttt--tgattacagGTGCGTACAAATACGTGTCGGAGCTATGGAGGAAGAAGCAGTCGGATGTGATGAGGTTTCTTCAGAGGGTTAGGTGTTGGGAGTATCGCCAGCAGCCTTC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------gtgagctcctcctccgacgccgcctccctccatcactctcgtc--tccagtttcccacccctccacctccatctctctcctgatccgt--cctccgtcgt-------------------tttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
              |     ||| || | |   |   |||   | |  ||    ||  | ||| ||| |     |        ||     | ||| | |||  |     | |                    |||| |    | ||||||||||||||| || || ||||||||||||| ||| ||||| || |||||||| ||| | ||| | ||  |||||||||||||||| ||||| ||  |
gtaaatccttcttctccatcccttcttctagatcaaatcctctcgtttcttagatcgattcagcttctccattgtttgttcaaatgatgtttctgttacgtatctgttattgcaaactacttagcttaatgatttgattgatatagGTGCGTACAAGTATGTATCTGAGCTATGGAGGAAGAAACAGTCCGATGTGATGAGATTCCTCCAGAGGGTTAGGTGCTGGGAGTACAGACAGCAACCTTC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 3'ss of exon 1
gtgagctcc---tcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
|| ||| ||      |||  | |   ||   ||    |||  |      |  ||         | |  |    ||  ||  |  |  | | |   ||||  ||   |    ||| || |||||||||||||||||||||||||||| |||||| || || |||||||||||| ||||| | ||| |||||||||||||  | ||||| ||  |
gtaagcaccaagctttccttcactctctttttct-ctacttccaagcggatattagggttttccgatttgtggcttcctgttatt--ggcattgttcgtggtggcat---tagGGGCTTACAAGTACGTGTCGGAGCTATGGAGGAAGAAGCAATCCGATGTGATGAGGTTCTTGCAGAGGGTGAGGTGCTGGGAGTATCGCCAGCACCCTTC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0551g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
     ||     | |   | |    |  |  || ||  | |  |     |       ||      |         |  | |   ||     ||   |||| | |  | ||| || ||||| |||||||| ||  ||||||||| |||||| || ||||||||||||||| ||||| | ||  |||| ||||||||| | || || ||| |
-----cttaatatgctgtgacagtgctttgaattacattggggtattaatggaggttccattgtatttggagtagtagtaagttgtg----gtgtatttggttta-atagGGGCTTACAAATACGTGTCCGAATTATGGAGGAAGAAGCAATCAGACGTGATGAGGTTCCTGCAGAGGGTTAGGTGTTGGGAGTACCGTCAACATCCGTC

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S152_141V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------gtgagctcct-cctccgacgccgcctccctccatcactctcgtctccagtttcccacccc----------tccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcac-agGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
                                                  | |   |  |   |           |   |   || || || | |  || ||  | |             || | ||  |  | | |  |  |   |  |   |  |||   | | | | |||||||||||||||| |   |||||| ||||||| ||||||||| || ||| || | ||| ||| ||| ||||| |||||||||||||||||||  || | 
gtattcattcccagctccctctctctctagcgctgcgtagctgcgtagctgcgtttttttattttttttattttttatttttttccctttccttttgaggtttgcgcagtgtgatcgagatctaactggagttttttttttttttttttttttttttttaaatttcctccagGTGCGTACAAGTACATCGAGGAGCTGTGGAGGAAGAAGCAGTCTGATGTGCTGCGTTTCTTGCTGCGTGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGG

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
               |     |  |       |   |        || ||            | |      |   | |   |   |      |  | ||| | |||  ||| |||||||||||| |    ||||||||||||| ||||||||| || ||| || | ||| |   ||| ||||| |||||||||||||||||||  || | 
--------ggttgttggtagtgtttttgattgttgattggaatgacatttagggttttgggaaacggtggttacatgcatgtttatgtcaaatgatcttgttctgc--agGCGCGTACAAGTACATTGAAGAGCTATGGAGGAAGAAGCAGTCTGATGTGCTGCGATTCCTATTGCGTGTGCGATGCTGGGAGTACAGGCAGCTCCCAGG

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S134_151V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagctcctcctc-cgacgccgcctccctccatcactctc-gtctccagtt-----tcccacccctccacctcca--------tctctctcctgatccgtcctccgtcgttttgctgtgcac-agGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
|| |||   | ||| |  |  |  | | |  |||   |||| || |  |  |     |  | ||   |||  | |         ||||   | | | |     |   | |||||| ||      |||||||||||||||| |   |||||| ||||||| ||| ||||| || ||| || | ||| ||| ||| || || ||||||||||||||||||| ||| | 
gtaagcaatttctcgcagcctctgccctcgtcatggatctctgtgtgtatgtggagctgacgcctgaccagattcggaatgaattctcaacctttaactagggttt-ttgttttgttgaattttagGTGCGTACAAGTACATTGAGGAGCTGTGGAGGAAGAAACAGTCCGATGTGCTGCGCTTCCTGCTGCGTGTTCGCTGCTGGGAGTACAGGCAGCTGCCCGG

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacctc---catctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
           || |||    ||  |  | || |  | | |  ||  |||           |   |     ||     | | |   | |  |   | |||||| | ||   ||| |||||||| ||| |   |||||||||| ||| ||||||||| || ||| || | ||| |||  || ||||| |||||||||||||||||||  || | 
-----------cttcgata--gctacgttgcaccggtgttgcttcatgttgttagtgttggcgaattgtgtatggggtttcggggtcttatttatttgttttggtttgtttagGGGCGTACAAATACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGATGTGTTGCGATTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGG

upper sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S7_364V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagctcctcctccgacgccgcctccctccatcactctcgtctccagtttcccacccctccacc--tccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
           ||  |  |  |  |       |    |   ||    |||    ||        |  |  || |      |  |  ||  |  ||   |||| | | | |||| |||||||||||| |   |||||||||| ||| ||||||||| |||||| || | ||| |||  || ||||| |||||||||||||| || |  || | 
----------gctttg-tgttgtttggtagggttgggccattcgatggttggtgacgagagagtccgttaatgttgggttttttttgtaatgtgtgaatttggt-tccccagGCGCGTACAAGTACATTGAGGAGCTATGGCGGAAGAAGCAGTCCGACGTGCTGCGTTTCTTGCTTCGTGTGCGCTGCTGGGAGTACAGACAACTACCCGG

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|29658150|gb|CB654425.1|CB654425
EST:     CCGCCGCCGCCATGG                         GTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGA
genomic: CCGCCGCCGCCATGGgtgagctcct ... ctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccctccacctccatctctctcctgatccgtcctccgtcgttttgctgtgcacagGTGCGTACAAGTACGTGTCGGAGCTATGGAGGAGGAAGCAGTCGGACGTGATGAGGTTCGTGCAGCGCGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGC
                    tcctgat  putative branch site (score: 3)
                                        ttttgct  putative PPT