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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 50
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 51
gtttgctatttcaatcctggaggtgt------ttaagctagtt---------ttggtgtt-tttaac---tgattggct--attatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
|||||  |  ||| || ||  || |       ||  ||| |||         | | |||| ||| ||    |||||  |  ||||   | ||||  | |||||||||||||||||||| || ||||||||||  || ||||| |||||||||||||| || || ||||| ||| | ||||||  ||||||||||||||| || |
gtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttg--taatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAATGCCTTCCAGTCTTCCATTATCCACGCCGCCCCCAATAGCAGCAATACCCAATCCAAAATTTGCACCATCCC

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 33
gtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactga-------ttggctattat--cgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
||| |  || ||| |  |||||| |||| |||| ||| |  |  ||||   |||       |||  | | ||  |||| || ||  |||||||||||||||||||| || ||||||||||| || || || |||||| | ||||| || || ||||| ||| | ||||| ||||||||||| ||||| || |
gttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgca-atgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 52
------------------------------------------gtttgctattt-caatcctggaggtgtttaagc-tagttt--tggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAAT---TGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
                                           |||||  |||  | | ||    | | ||  |  ||||    | | || ||| ||  |||||| |||    |||     |  ||||| |||||||||||||||| |||||||||||||| || ||  | ||  |  | || ||||| ||      |  |  |||| | |||||  | |||||||||    
gttgagttaatttacttgtactaacacatgttcttaattggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgac-aattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC---

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 53
-----------------------------------------gtttgctattt-caatcctggaggtgtttaagc-tagttt--tggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAAT---TGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
                                           ||||  |||  | | ||   || | ||  |  ||||    | | || ||| ||  |||||| |||    |||     |   |||| |||||||||||||||| |||||||||||||| || ||  | ||  |  | || ||||| ||      |  |  |||| | || ||  | |||||||||    
gttgagttaatttacttgtattaccacatgttcttaattgaacttgcattttgtatttctaccggcgattgggagtagtagaattgagtatttgacc-attggcaattgat-tttaacattttggcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCGAGTTTACCGATGCCAACCCCTCCACCGGCATCTTTAAATATATCTTCCCCTGATTTTGCACCTC---

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|58658439|gb|CK047119.1|CK047119
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58601380|gb|CK011908.1|CK011908
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCA
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCA
EST: gi|58675157|gb|CK063844.1|CK063844
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|218497579|gb|FG955134.1|FG955134
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58677253|gb|CK065940.1|CK065940
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctagttttggtgtttttaactgattggctattatcgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC
             tgtttttaa  TA-rich tract