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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaacttagtctggcatctttttgcttatttgagttcttaatgcaatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT

Basic information

species Oryza sativa
transcript LOC_Os11g25980.2
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G479163_T01 (Zea mays), 3'ss of exon 3
gtaagtcaaacttagtctggcatctttttgcttatttgagttcttaatgcaatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaat-gttctcattttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT
                                            |||  ||  |    ||        | |    |||   | | |     | | ||||  | || |  || | ||  ||| | |||||||||||||||||||||||| || ||||||||||||||  |||||||||| |||||||||||||||||||| || ||||||||||||||||||||| ||||||||
-------------------------------------------gtaagccataaaccgtccgtacttgtattatggtagttggacgtatagtgtgtgctagttttcttgattgctcatattctgtgcatgcagTTTTTCTTTTCTTTCAGGCATTGCTGGAACAAGCTTATTCAACTCAGTTAGTTTGATGGCTTATAATGTTTTCTACACAAGCATTCCTGTTTTAACTACT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 21
gtaagtcaaacttagtctggcatctttttgcttatttgagttcttaatgcaatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcatt-ttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT
                      | ||  || ||||    ||||| |||||  ||| ||   ||  | |||| | | ||         | ||| ||| ||    || |||| || || ||  ||     | ||||||||| ||| |||| ||| |  ||||||| || || ||||| || ||||| |||||||||||||| || ||||| || ||  |||||||||||  || |
--------------------attgttaatgattatgaatgttct-aatgc--tag-atgggcatccaatttctttata---------tagatctattctaaatttttcaaggtactgatgattgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 21
gtaagtcaaacttagtctggcatctttttgcttatt-tgagt-tcttaatgc--aatagtattctcagtccatttatctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT
                        || || || ||| ||| | |  ||||||   ||||   |  || |   |||||   || |   || ||  | ||    ||    ||   ||| |  | ||||       ||||||||| ||| |||| ||| |  ||||||| || || ||||| || ||||| |||||||||||||| || ||||| || ||  |||||||||||   | |
------------------------ttgttactgattatgaatgttctaatgctagataggcattccaatttctttat--atagatctattctaaaaat---tttaaggtactgatggttgcctttt-------cagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT

upper sequence: LOC_Os11g25980.2 (Oryza sativa), 3'ss of exon 21
lower sequence: AT5G44240.2 (Arabidopsis thaliana), 3'ss of exon 20
gtaagtcaaacttagtctggcatctttttgcttatttgagttcttaatgcaatagtattctcagtccatttat-ctgtaaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT
                                                    ||   || | |   ||  |||  | | |    ||       |  |  |||    |  | ||    ||    ||  ||| || || || ||| |||| ||  || ||||||| ||||| ||||| || |||||  |||||||||||||||| |||||||| ||  ||||||||||   || |
---------------------------------------------------gtaagtttattatctcagatatgttctcagtagatatcattcaagtcgttcatgaaatactgacaacag--aatctatgtagCTTCTCGTTTATTTCAGGCGTTTCTGGAACCAGTCTTTTCAATTCAGTTAGCCTGATGGCTTATAACGTTTTCTACACCAGTGTTCCTGTTCTTGTTAGT

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|163929268|gb|EG711029.1|EG711029
EST:     TCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACT                         TTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAG
genomic: TCTCAGTATTCTTTCTACAAGTCATTGTTAATTTGCTTTATCCAGATACTgtaagtcaaa ... atgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagaatgctggatatatgcttctcttatcaatgttctcattttatgcatgcagTTTTTCTTTTCTTTCTGGTATTGCTGGAACAAGTCTATTCAACTCGGTTAGTTTGATGGCTTATAACGTCTTCTACACAAGCATTCCTGTTCTAACTACT
                                      tcattttat  TA-rich tract