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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcaccttctctggtcaatgcatgcctgaacgtgtagtgttgcagcattatatcttttaaaatgcatggagcttatgaatcttgctataacaatttcagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATACCCCCGGACGAAATAGGTGTCACCTTTGAGGACATTGGGGCATTGGAAA

Basic information

species Oryza sativa
transcript LOC_Os03g22420.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 20
----------------------------cttcaccttctctggtcaatgcatgcctgaacgtgtagtgttgcagcattatatctt-ttaaaatgcatggagcttatgaatcttgctataacaatttcagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATACCCCCGGACGAAATAGGTGTCACCTTTGAGGACATTGGGGCATTGGAAA
                            ||  | |   |     ||   || | ||  | ||  |   |   ||  ||  |  || ||  | || || |||||||    |||  || ||||||| ||||||||||||||| || ||||| ||||||||| | |||||||| |||||||| || ||  | ||||| ||||| ||||||||||||||||| || || ||||
gtagtcattttcttttgttatattaggactcgaacccgttaatccagctca-gtctctatgttgatcttcagagttttggaaattgttttactgtatagagcttactgttct--ctctaacaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
---------------------------------------cttcaccttctctggtcaa----tgcatgcctgaacgtgt------agtgttgcagcattat-atcttttaaaatgcatggagcttatgaatcttgctataacaattt---cagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATACCCCCGGACGAAATAGGTGTCACCTTTGAGGACATTGGGGCATTGGAAA
                                       | |||  || | |||  |     |||||  ||    || |      ||| |     | || | || |||| || ||   |    | |    | ||  |  ||   |||   |||||| | | |||||||||||||||||| ||   |||||||||||||||||| || ||    || || || ||||| ||||| || ||||| || || ||||
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 15
---------------------------------------cttcaccttctctggtcaa----tgcatgcctgaacgtgt------agtgttgcagcattat-atcttttaaaatgcatggagcttatgaatcttgctataacaattt---cagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATACCCCCGGACGAAATAGGTGTCACCTTTGAGGACATTGGGGCATTGGAAA
                                       | |||  || | |||  |     |||||  ||    || |      ||| |     | || | ||  ||| || ||        | |    | ||  |  ||   |||   |||||| | | |||||||||||||||||| ||   |||||||||||||||||| || ||   ||| || || ||||| ||||| || ||||| || || ||||
gtaatttaatattagatgttacaattataaacctttctccatcatattttgtggagatattttgcattactactggtatccatctagtttctttaccttgtcatgatttgaattgtggaattgtcacctgtattctttgaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCGCCAACCGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

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|163925949|gb|EG712301.1|EG712301
EST:     ACATAAGGAAGTCGCTCAAG                         GATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATA
genomic: ACATAAGGAAGTCGCTCAAGgtgatatact ... acaatttcagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATA
EST: gi|58688470|gb|CK077157.1|CK077157
EST:     AAAGTGTGGAATCTAACCCTAAGAGCAGCAACATAAGGAAGTCGCTCAAG                         GATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATA
genomic: AAAGTGTGGAATCTAACCCTAAGAGCAGCAACATAAGGAAGTCGCTCAAGgtgatatact ... acaatttcagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATA
EST: gi|58605943|gb|CK033976.1|CK033976
EST:     AAAGTGTGGAATCTAACCCTAAGAGCAGCAACATAAGGAAGTCGCTCAAG                         GATATTGCTACTGAGAATGACTTTGAAAAGCGACTTCTTGCTGATGTTATA
genomic: AAAGTGTGGAATCTAACCCTAAGAGCAGCAACATAAGGAAGTCGCTCAAGgtgatatact ... acaatttcagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATA
EST: gi|29635827|gb|CB640836.1|CB640836
EST:     AAAGTGTGGAATCTAACCCTAAGAGCAGCAACATAAGGAAGTCGCTCAAG                         GATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATA
genomic: AAAGTGTGGAATCTAACCCTAAGAGCAGCAACATAAGGAAGTCGCTCAAGgtgatatact ... acaatttcagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATA
EST: gi|58662327|gb|CK051007.1|CK051007
EST:     AGGAAGTCGCTCAAG                         GATATTGCTACTGAGAATGAATGGGGAAAAGCGACTTCTTGCTGATGTTAT
genomic: AGGAAGTCGCTCAAGgtgatatact ... acaatttcagGATATTGCTACTGAGAATGAAT-TTGAAAAGCGACTTCTTGCTGATGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattatatcttttaaaatgcatggagcttatgaatcttgctataacaatttcagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATACCCCCGGACGAAATAGGTGTCACCTTTGAGGACATTGGGGCATTGGAAA
                                        ctataac  putative branch site (score: 3)
     atatcttttaaaat  TA-rich tract