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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagaaatgcatcccctattgctagctgtacaaacatgacatgtttcccttgttccttccaatccctcaagaattatcttcttcaatgattaattgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTTCGGAAGCTCTTGAATATGGACTAGTCGGTGTGAACGAGGGGATCATCTC

Basic information

species Oryza sativa
transcript LOC_Os02g07760.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G119482_T01 (Zea mays), 3'ss of exon 17
---tgtagaaatgcatcccctattgctagctgtacaaacatgacatgtttcccttgttccttccaatccctcaagaattatcttcttcaatgattaat-tgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTTCGGAAGCTCTTGAATATGGACTAGTCGGTGTGAACGAGGGGATCATCTC
     ||  |||| ||    |    |      |||||    ||| | | |||||||||   ||  |||  |||||||||     |  |  || |  || |||||||||||||||||| || || || ||||||||||||||||||||||| || || ||| ||||||| || ||  |||| || || |||||||| || || ||
accgctaacaatggattatgtggatcattgcctacaatgtagacttatctcccttgttatgtctgatc--tcaagaatt--tccccactgtgctggatctgcagGCTTAGCTGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCTGAATCTCTTGAGTACGGCTTAGTTGGGGTAAACGAGGGAATTATTTC

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G128114_T01 (Zea mays), 3'ss of exon 17
----tgtagaaatgcatcccctattgctagctgtaca-aacatgacatgtttcccttgttccttccaatccctcaagaattatcttcttcaatgattaat-tgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTTCGGAAGCTCTTGAATATGGACTAGTCGGTGTGAACGAGGGGATCATCTC
    | ||  |||| |     ||| | |   |||  | ||  |    | | ||| |||||   ||  |||  ||||| |||  |   ||   || |  || | |||||||||||||||| || || || ||||||||||||||||||||||| || || ||| |||||||||| ||  |||| || || ||||||||||| || ||
tacctctaacaatggaaga--tatggatcattgtctacaaagtagattatctccattgttatgtctgatc--tcaagcatttccccatt--gtgctggatatacagGCTTAGCTGCATACATATTTACCAAGAGCATACCTCGTTCATGGCGTGTATCCGAATCTCTTGAATACGGCTTAGTTGGGGTAAACGAGGGGATTATTTC

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv19s0085g00870.t01 (Vitis vinifera), 3'ss of exon 16
--tgtagaaatgcatcccctattgctagctgtacaaacatgacatgtttcccttgttccttccaatccctcaagaattatcttcttcaatgattaattgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTTCGGAAGCTCTTGAATATGGACTAGTCGGTGTGAACGAGGGGATCATCTC
   ||   |||   || || |    |    ||| |   ||   |||       | | | |    |    | |  |  | | ||     |    || ||||||| |||||||| ||||| |||||||| | | |||  || || ||||| || || |||| ||||||||||||||| || ||||| |  || ||  | ||  |
atggtcttaatcattctcccaaatgtcatggtaaatggatt-tatgaaaaggatatccatctagacttataatcatgtgtttttcatgacacata-ttgcagGTTTAGCTGCCTATATTTTCACAAAAAACCTACAACGATCTTGGCGTGTCTCTGAAGTTCTTGAATATGGACTTGTTGGTGTCAGTGAAGGATTAATTCC

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|86496493|gb|CI139126.1|CI139126
EST:     ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAG                         GCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT
genomic: ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAGgttcgttact ... ttaattgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT
EST: gi|218485663|gb|FG949794.1|FG949794
EST:     ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAG                         GCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT
genomic: ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAGgttcgttact ... ttaattgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT
EST: gi|88227449|gb|CI226929.1|CI226929
EST:     ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAG                         GCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT
genomic: ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAGgttcgttact ... ttaattgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT
EST: gi|218498992|gb|FG968229.1|FG968229
EST:     ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAG                         GCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT
genomic: ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAGgttcgttact ... ttaattgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT
EST: gi|218482143|gb|FG968613.1|FG968613
EST:     ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAG                         GCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTCT
genomic: ATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAGgttcgttact ... ttaattgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccttgttccttccaatccctcaagaattatcttcttcaatgattaattgcagGCTTAGCTGCATATATCTTCACAAAGAGCATACCTCGTTCATGGCGCGTTTCGGAAGCTCTTGAATATGGACTAGTCGGTGTGAACGAGGGGATCATCTC
                                           gattaat  putative branch site (score: 3)
                                     ttcaatgattaatt  TA-rich tract