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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag

Basic information

species Oryza sativa
transcript LOC_Os11g06390.6
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G006765_T02 (Zea mays), 5'ss of exon 2
------GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag
         | ||||| | |||| |   ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| || || ||  |||    |  ||| |  |  |||| |      ||||    | ||||||||  ||               | || | |||||||
TGTTTTTGTTCCAGAATCTGTAGCA---AATGGCTGACGGCGAGGACATCCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAGgtttgtagttcttgttcacgctgcttcatgtt--cagtaacat---tgttctgttaatttaatcacat-------------cacaaactactggcag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G126190_T03 (Zea mays), 5'ss of exon 2
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag
                  |  ||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||||||| || || ||  ||| |  |  | |||  ||     |    || | ||    | ||||||||  |        ||||||| | || |  ||||||
-----------------TAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAGgtttgtagttcttgttcatgctggtacttcatatt--ctgcaacctttttctgctaatttaatcacacg------ttttcttacaaactattggcag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G126190_T02 (Zea mays), 5'ss of exon 2
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag
         | ||  || |  ||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||||||| || || ||  ||| |  |  | |||  ||     |    || | ||    | ||||||||  |        ||||||| | || |  ||||||
--------CATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAGgtttgtagttcttgttcatgctggtacttcatatt--ctgcaacctttttctgctaatttaatcacacg------ttttcttacaaactattggcag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA04G39380.2 (Glycine max), 5'ss of exon 2
GAATTCAGAACCAGT--AGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag
            |||   | |  | |||||||| |  ||||| || || |||||||| ||||||||||||||||| ||||| |||||| ||  |   || |        || | ||||   |  |||     || |  ||    | |||  |   |||| || | |   ||  ||    |||
-----------TAGTTTGGTAAAAGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAGgttagtactttgcagtttcttctgttatgtgtaattgc-atctattagtctcggtttcgttatcaaacgatttatttctataatgatctgtgtacag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G32220.1 (Glycine max), 5'ss of exon 1
------------------GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtata-ctttacttttcttgcgaattgctggcag
                  |  ||  | |    | | |  | ||||| || |  ||||| || || |||||||| ||||||||||||||||| ||||||||||||    || || |   |   | ||| |||||  ||  |         | |    |  || |    ||| ||  |  |||  |   |||      |||
TATTTCATGGCACCCTATGCTTTTTGCAG-GTTTGTAAAAGATGGCCGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTCAAGgtt---agtacttagcggctttgttt-tttgtttcatgtgcttgtgcatctgctagccttgagttcataactgaatctttgattttaatatggaacag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G15480.1 (Glycine max), 5'ss of exon 2
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagtt--atccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag
              | | |  | ||||| || | |||||| || || |||||||| || |||||||||||||| |||||||||||| ||  |  || |  | | | ||  ||||| |||  |  ||   || || |        |||  | ||| |||| |||  |   |||  |       
------------GTTTGTAAAAGATGGCAGATGCCGAGGATATTCAACCCCTTGTTTGCGACAATGGAACTGGAATGGTCAAGgttagtact--tcgt--ggatttttgttttgttgcatgtgcatatgcaagtcttgagttcataagtgaataatttattttaatatggaacag-------

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA04G39380.1 (Glycine max), 5'ss of exon 2
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag
              | | |  | |||||||| |  ||||| || || |||||||| ||||||||||||||||| ||||| |||||| ||  |   || |        || | ||||   |  |||     || |  ||    | |||  |   |||| || | |   ||  ||    |||
------------TTTGGTAAAAGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAGgttagtactttgcagtttcttctgttatgtgtaattgc-atctattagtctcggtttcgttatcaaacgatttatttctataatgatctgtgtacag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA06G15520.2 (Glycine max), 5'ss of exon 2
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag----
              | | |  |||||||||| |  ||||| || || |||||||| ||||||||||||||||| ||||| |||||| ||  |      | | ||| | |  ||   | | ||    | || |     || ||| ||  | | ||  | || | |     ||     |       
------------TTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAGgttagtact------ttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattat-tgctcaatttatttaaatgatcatctgtgtacag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G32220.2 (Glycine max), 5'ss of exon 2
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtata-ctttacttttcttgcgaattgctggcag
              | | |  | ||||| || |  ||||| || || |||||||| ||||||||||||||||| ||||||||||||    || || |   |   | ||| |||||  ||  |         | |    |  || |    ||| ||  |  |||  |   |||      |||
------------GTTTGTAAAAGATGGCCGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTCAAGgtt---agtacttagcggctttgttt-tttgtttcatgtgcttgtgcatctgctagccttgagttcataactgaatctttgattttaatatggaacag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 5'ss of exon 2
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtg-atttaatcgtatactttacttttcttgcgaattgctggcag
                     ||||||| || || ||||| || ||||| ||||| ||||||||||||||||| ||||| |||||  ||    ||  ||  |     | || | | |   | | |  | |  || |     | |||   ||    | |   || |||   |||    |   
-----------------TGAAAAATGGCCGATGGTGAGGATATTCAGCCACTTGTCTGTGACAATGGAACTGGAATGGTGAAGgtgagttagact-gtttatttagatactgtatggttctaaccttctttgttgtacatgtgtaagactactgatcatgatttttgtatattaacag---

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 5'ss of exon 3
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg-----ctcattcgtagtatttctttgtagcagttatcccca-tgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag
            | ||  ||||  |||| ||    || || ||||||||||| || ||||||||||||||||| ||||| |||||  || ||      ||   | |   |     ||||| |   |  |  |   |  | |  || |  | | | |||   |     | ||  |  ||    ||||
----------GTAATAAAAGGA--TGGCCGATACTGAAGATATCCAGCCCCTCGTCTGTGACAATGGAACTGGAATGGTGAAGgtctgttgtttctttcttgcttgatatgcagatttgttgtgttgtttgctgctcctcaaatgctcaatttgaataagctttccatgttatgctttatatgcag

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 5'ss of exon 1
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagt-atttctttgtagcagttatccccatgtttatg--tgatttaatcgtatactttacttttcttgcgaattgctggcag---
             ||   || | ||||| || | |||||| |||||||| ||||||||||||||||||||||| |||||||||||| ||     | |||| || | |||||  || ||    |||     ||| |     || ||  ||      |||||    | || | || ||          
-----------AGGTTTTAGAAGATGGCCGATGCCGAGGATATCCAGCCTCTTGTGTGTGACAATGGAACTGGAATGGTCAAGgtttgt--cagttattcttatttatttcaatg-agttcatatgtttgtgtctgcacttgtttagataaagggctttagggattttacaaaatgaatttgactc

upper sequence: LOC_Os11g06390.6 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 3
GAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtgctcattcgtagtatttctttgtagcagttatccccatgtttatgtgatttaatcgtatactttacttttcttgcgaattgctggcag--------
           | |||  | |||||||||||||| |||||  | |||||| | ||||| |||||||||||||| |||||||||||     | | ||| || |   |   |     |  |  | | || |  ||  |    |  | ||    | | ||   |  |       |||||  |         
---------GTCGGTATTAAGAAATGGCTGACGGTGAGGAAGTACAGCCCTTGGTGTGCGACAATGGAACTGGAATGGTCAAGgt-----gaggtcactcttctaaaacccagagattaacttttccgaacttggttcattggattcaaggattctataatcttgagcttctgctgaaaaatattcta

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|58669469|gb|CK058155.1|CK058155
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|58659094|gb|CK047774.1|CK047774
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|218491871|gb|FG949270.1|FG949270
EST:     CAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
genomic: CAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|58601398|gb|CK011926.1|CK011926
EST:     CGAGGACATCCAGCCCCTTGTGTTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCANGGCTGTTTTCCCTAGTATCGTG
genomic: CGAGGACATCCAGCCCCTTGTG-TGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|58690729|gb|CK079416.1|CK079416
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGTGCTGTTTTCCCCTAGTATCGT
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTT-CCCTAGTATCGT
EST: gi|58607922|gb|CK035955.1|CK035955
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGTGCTGTTTTCCCTAGTGTCGTG
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
EST: gi|29643809|gb|CB648816.1|CB648816
EST:     GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG                         GCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG
genomic: GCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAGgttcgtggtg ... ttgctggcagGCTGGGTTTGCTGGGGACGATGCGCCCAGGGCTGTTTTCCCTAGTATCGTG