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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactccagtatccaatccagagtcacctcttgtacagatgccagtgtatacatatctaaaatctaagtttcacaatcgaaacatcattgatcaattgttgtctattaatgccagTTTACAGGAAAGCAGAGGATATGAATTATCACTCTGTATGTTTGCATGTTCTTGCCGATTCAGTACGGAG

Basic information

species Oryza sativa
transcript LOC_Os02g58580.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G017365_T08 (Zea mays), 3'ss of exon 5
gtaagtactcca-gtatccaatccagagtcacctcttgtacagatgccagtgtatacatatctaaaatctaagtttcacaatcgaaacatcattgatcaattgttgtctattaatgccagTTTACAGGAAAGCAGAGGATATGAATTATCACTCTGTATGTTTGCATGTTCTTGCCGATTCAGTACGGAG
    ||||   | | | |  ||     ||  | ||| || || |||    | | ||| | | |    |  |||  |   ||   |||||  |||               || | || ||||||||||||| ||||||||||||||||| ||||| || |||||||||||  | || |||||| |||||||
----gtacgggaagcaacttatatcctgttgcttctggtgcaaatggagatttgtacttgtttccc-tgcaagggttgtaaattaaacagaatt---------------atgattggcagTTTACAGGAATGCAGAGGATATGAATTACCACTCGGTCTGTTTGCATGTGTTGGCAGATTCAATACGGAG

upper sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0007g06550.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtactccagtatccaatccagagtcacctcttgtacagatgccagtgtatacatatctaaaatc-taagtttcacaatcgaaacatcattgatcaattgttgtctattaatgccagTTTACAGGAAAGCAGAGGATATGAATTATCACTCTGTATGTTTGCATGTTCTTGCCGATTCAGTACGGAG
                   || |  |||    |  ||| |||| |  |   |   ||   |||    |  | | || |   |    |  |  ||| |||  | |  | | | | ||| ||| ||||||||||||||||||||||| || ||||| || || |||||||||||||| |||||  |||| ||
-----------------agattcttagtgttgtagtgttcaga-gttatgattgtcagccctaggtgcacatgctttattttttggatgttcttg-tcatctttcatttttcattgc-agTCTACAGGAAAGCAGAGGATATGAACTACCACTCAGTTTGCTTGCATGTTCTTGCAGATTCTATACGCAG
















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|29661173|gb|CB657448.1|CB657448
EST:     TAATTTACTTGGTGTTTGGTTCTTTCGGAGCTATGCTCGTGTTAACATAG                         TTTACAGGAAAGCAGAGGATATGAATTATCACTCTGTATGTTTGCATGTTC
genomic: TAATTTACTTGGTGTTTGGTTCTTTCGGAGCTATGCTCGTGTTAACATAGgtaagtactc ... ttaatgccagTTTACAGGAAAGCAGAGGATATGAATTATCACTCTGTATGTTTGCATGTTC
EST: gi|29656007|gb|CB652282.1|CB652282
EST:     TAATTTACTTGGTGTTTGGTTCTTTCGGAGCTATGCTCGTGTTAACATAG                         TTTACAGGAAAGCAGAGGATATGAATTATCACTCTGTATGTTTGCATGTTC
genomic: TAATTTACTTGGTGTTTGGTTCTTTCGGAGCTATGCTCGTGTTAACATAGgtaagtactc ... ttaatgccagTTTACAGGAAAGCAGAGGATATGAATTATCACTCTGTATGTTTGCATGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctaagtttcacaatcgaaacatcattgatcaattgttgtctattaatgccagTTTACAGGAAAGCAGAGGATATGAATTATCACTCTGTATGTTTGCATGTTCTTGCCGATTCAGTACGGAG
                                           tattaat  putative branch site (score: 2)
                                         tctattaat  TA-rich tract