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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagatcattccttttgttgcacatcacagtgtccatccaagggatttgcagaattatgtgcgggcgagctagctttggtacagtgaaaaaactgaattatgtgcaatccattttggtgctcacatagttatattctgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG

Basic information

species Oryza sativa
transcript LOC_Os04g51400.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51400.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G140924_T01 (Zea mays), 3'ss of exon 3
gtaaagatcattccttttgttgcacatcacagtgtccatccaagggatttgcagaattatgtgcgggcgagctagctttggtacagtgaaaaaactgaattatgtgcaatccattttggtgctcacatagttatattctgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG
                                         |||  |||     | || |||    ||    |||   || || |||     | | ||  ||||   |        ||    ||  ||  ||| ||| ||    ||||||  ||||||| || |||||||  |||||| ||||||| ||||| ||||| || ||||||||||| || || 
---------------------------------------gtaagacattct---atttctgtcactgcacaatagtcgtgcta-agtcc---agcagagctatgaagagaa-----tgcaaatcgtatgattacattgtgcactgcagCTCCAGAACTATTTAATATTCAGCGATCGGCACAGAGGAATGAGGATGGATATCGACGGCATGTCCTACGAA

upper sequence: LOC_Os04g51400.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G053909_T01 (Zea mays), 3'ss of exon 3
gtaaagatcattccttttgttgcacatcacagtgtccatccaagggatt-tgcag-aattatgtgcgggcgagctagctttggtacagtgaaaaaactgaattatgtgcaatccattttggtgctcacatagttatattctgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG
                          | |    ||| ||    |  | |   ||  | | |||    | | |||    |||  | |  |  |    |  | |   |   | ||   |   ||  |    |   |||||| ||| | |||||| |||||||| |||||||||||||||||| | ||||| ||||| ||||| || ||||||||||| || || 
-------------------------gtaaggcggtctatttctgtcactacacaacagtaatgctaagtccagcagagttt--ttcttttgattttccaagtccagcagagtcatgtagagtatttctgtcactatattgtgtgttgcagCTCGAGAACTATTTCATATTCAATGATCGGCATAGAGGAATGAGGATGGATATCGACGGCATGTCCTACGAA
















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|29676639|gb|CB672914.1|CB672914
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|58691609|gb|CK080296.1|CK080296
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|89196993|gb|CI021833.1|CI021833
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGGAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29666124|gb|CB662399.1|CB662399
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29671277|gb|CB667552.1|CB667552
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29666123|gb|CB662398.1|CB662398
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29676637|gb|CB672912.1|CB672912
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29626982|gb|CB631993.1|CB631993
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|86841641|gb|CI337348.1|CI337348
EST:     GGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: GGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|9865894|gb|AU101644.1|AU101644
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgaattatgtgcaatccattttggtgctcacatagttatattctgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG
                          tgctcac  putative branch site (score: 2)
                                          ttctgtctc  putative PPT
                                 atagttatatt  TA-rich tract