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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaatattgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta...

Basic information

species Oryza sativa
transcript LOC_Os08g33830.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G178169_T01 (Zea mays), 5'ss of exon 9
AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaata-ttgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta----------
||| |||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  |||||||||| |||||||||||  ||||| || ||||  |||||||  |  |         |||| || |||| |||||    |||| |||          
AGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaattgtagtttcaggttgtgtaaattagcaaataatttaagt--atatatcgttcaa---------gactgataaataatgaattctgctcacttagtaaaaaaga

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G082174_T05 (Zea mays), 5'ss of exon 7
-------------AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaata-ttgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta
             ||| |||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||||  ||||||||||||||  ||||| || ||||| |||                                                 
ATATAACTACCGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTgtaagcttcatctgtcatactctcgtcatactgatctcaatgtaaaggtataaatagtagttttgggctgtgtaaattagcaaataatttaagtatatac------------------------------------------------

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G082174_T03 (Zea mays), 5'ss of exon 10
AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaata-ttgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta----------
||| |||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||||  ||||||||||||||  ||||| || ||||| |||   | ||| |         ||||||||||||  ||||    |||| |||          
AGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatagtagttttgggctgtgtaaattagcaaataatttaagtatata---ctgttcag--------gactaatgaataacgaattctgctcaattagtaaaaaaag

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA09G37080.1 (Glycine max), 5'ss of exon 10
AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaatattgaagt-acatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta
| ||| ||||| | ||||| | || ||||| |||||||||||||| || || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||     || |      ||  |  ||  | |  |   || | | | ||    |   | |||   |   || |  |  | ||     |  | ||   
ATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaaaatatgtgtttatgagttaatgttcttgaggaaaaaaatgaaaaatgggggaatattaaagatatccttagaagcaatgtggacacttgatcg-

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA11G21330.1 (Glycine max), 5'ss of exon 9
AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaatattgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta
| ||| ||| ||| ||||| |    ||||| |||||||||||||| || |  |||||||||| ||| |||||||||| |||||||||| | || ||||||||||||||     ||   |   |  |||  | | |||    | ||      ||  | |  ||| ||     |      |||  |     | |   || | 
AACAGCTGCCAAAAAAGCTCTAATGGGGCATTGCATATATGATGGTGGCTGTTGTAAGCTTCGTCTATCATACTCTCATCATACTGATATTAACGTAAAGgtataaattcatcttgatgagggaataatatgagaaaagggggagggggattagaattatacttatatgcaatgtgaaaattttcttgatcagaaatatt

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA18G49580.1 (Glycine max), 5'ss of exon 9
AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaatattgaagtacatatatcagttg-actaattgttgactaatgaatagtgaatgtaactcattta
  ||| ||||| | ||||| | || ||||| |||||||||||||| || || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||     || |      ||  |  ||  | |      || |  | |     |    | |||   |   || |  |  | ||     |  | ||   
-TCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGGtataaaaatatgtgtttatgagttaatgttcttgaggggaaaaatgaaaaaggggggaatattaaagatatccttagaagcaatgtggacacttgatcag

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G01150.2 (Arabidopsis thaliana), 5'ss of exon 7
AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaatattgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta-----------------------------------------------------------------------
|||| | || ||| ||||  ||||||| |||||||| ||||| || || |||||||||||||  || ||||||||||||||||||||||| ||||| |||||| | | |||   ||     | || | ||   ||  ||   ||  | | |  |  |  |   |     |    |  |||| | | |||   ||   ||                                                                        
AGCAATGGCCAAAGAAGCACTGGAAGGACACTGCATTTATGACGGTGGCTACTGTAAGCTTCGACTATCATACTCTCGTCATACTGATCTGAATGTTAAGgtacataagatttgttgcttttttg-agatgtgtacctaaaaaaaaaaacaattgtgaggggaagagaatagtaacggaattgcgtatgcttctttcttttctacatttcgcagcaaaatattaaatcaacgtctaattatcttcttcaattttcctgtgattgaatgaag

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 9
AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgtgtaaattaataaatattgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta-----
||||||||| ||| ||||| | || || ||||||||||||||||| || || |||||||||||||| |||||||||||||||||||||||||||||||||||||||||| |  |||       | |  || |  ||| | | |       | |   ||  | |  |  ||     | ||| |||| ||     | ||  |     
AGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatg-tgattttgattaatattcatgagaaaaaaataagaggggaaaaaatgtaaagtcttccttag---aagaaaagtggatccg-ttgatcgaaaaaa

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S326_1V6.1 (Physcomitrella patens), 5'ss of exon 9
------AGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatgatagtttcaggctgt-gtaaattaataaatattgaagtacatatatcagttgactaattgttgactaatgaatagtgaatgtaactcattta-
      ||  |  || ||| ||||  | ||||| |||||||| || ||||| |||| ||| ||||||||||| ||||||||||| ||||||||| | |||||||||||||      |  | |  |  ||| |  |    ||  ||  |||  |   |||    || |||  |   |  |  | | ||| ||   | | ||  | | | 
TACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGATTTAAATgtaaaggtattctccttcttgtaggtttgttgctagcccatgcatgatgacttcactat----gtggac--agcatctaaaattaaatcgtc--tctgacctaatcat

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|29677646|gb|CB673921.1|CB673921
EST:     ACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAG                         GCACATGATGAGAGAAGCAGAGACTACACTGTTTCATCAGATCCTAGTGCA
genomic: ACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatga ... ttacattcagGCACATGATGAGAGAAGCAGAGACTACACTGTTTCATCAGATCCTAGTGCA
EST: gi|218479197|gb|FG960287.1|FG960287
EST:     ACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAG                         GCACATGATGAGAGAAGCAGAGACTACACTGTTTCATCAGATCCTAGTGCA
genomic: ACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatga ... ttacattcagGCACATGATGAGAGAAGCAGAGACTACACTGTTTCATCAGATCCTAGTGCA
EST: gi|29675192|gb|CB671467.1|CB671467
EST:     ACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAG                         GCACATGATGAGAGAAGCAGAGACTACACTGTTTCATCAGATCCTAGTGCA
genomic: ACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGATCTCAATGTAAAGgtataaatga ... ttacattcagGCACATGATGAGAGAAGCAGAGACTACACTGTTTCATCAGATCCTAGTGCA