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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaattggtgttatgcacctatgcctcaatctctgattgtctgtatcaaatattaatcttattcatttgtacctttttcttataatcccttggatccagGTTTCTCCTCCTTCAGTGAGGGGCACATATGGGAGCTTTGTTCAGATTGCAACCTGCCTTGGAATCGTAGTATCTCTCCTAATTGGTACACCTGTGAAGG

Basic information

species Oryza sativa
transcript LOC_Os02g17500.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G412899_T01 (Zea mays), 3'ss of exon 1
gtatgtaattggtgttatgcacctatgcct--------caatctctgattgtctgtat------caaatattaatcttattcatttgtacctttttct---tataatcccttggatccagGTTTCTCCTCCTTCAGTGAGGGGCACATATGGGAGCTTTGTTCAGATTGCAACCTGCCTTGGAATCGTAGTATCTCTCCTAATTGGTACACCTGTGAAGG
|||||||  |  |||| | |||  ||| ||           ||||  || || |   |      |  |||    | | ||   || ||  || | | |   ||       | | || |||||||||||| || |||||||||| |||||||| ||||||||||||||||||||||||||||||||  ||||||| || || |||||||||||||| || |
gtatgtagatcctgttttccacaaatgactatcgataatgttctcatatggtttactttctactcggataaagttttcatcagttggtctctgtctatgtctacgtctgatggaatgcagGTTTCTCCTTCTACAGTGAGGGGTACATATGGTAGCTTTGTTCAGATTGCAACCTGCCTTGGAATTATAGTATCACTACTCATTGGTACACCTGTCAAAG
















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|29643521|gb|CB648528.1|CB648528
EST:     GAACAGGGATGGGATTAGGTCCACCAGTAGCTTCACTGTACATAACAGAG                         GTTTCTCCTCCTTCAGTGAGGGGCACATATGGGAGCTTTGTTCAGATTGCA
genomic: GAACAGGGATGGGATTAGGTCCACCAGTAGCTTCACTGTACATAACAGAGgtatgtaatt ... ttggatccagGTTTCTCCTCCTTCAGTGAGGGGCACATATGGGAGCTTTGTTCAGATTGCA
EST: gi|88362011|gb|CI607011.1|CI607011
EST:     TGGGATTAGGTCCACCAGTAGCTTCACTGTACATAACAGAG                         GTTTCTCCTCCTTCAGCTGAGGGGCACATATGGGAGCTTTGTTCAGATTGC
genomic: TGGGATTAGGTCCACCAGTAGCTTCACTGTACATAACAGAGgtatgtaatt ... ttggatccagGTTTCTCCTCCTTCAG-TGAGGGGCACATATGGGAGCTTTGTTCAGATTGC
EST: gi|218499348|gb|FG943597.1|FG943597
EST:     GAACAGGGATGGGATTAGGTCCACCAGTAGCTTCACTGTACATAACAGAG                         GTGTCTCCTCCTTCAGTGAGGGGCACATATGGGAGCTTTGTTCAGATTGCA
genomic: GAACAGGGATGGGATTAGGTCCACCAGTAGCTTCACTGTACATAACAGAGgtatgtaatt ... ttggatccagGTTTCTCCTCCTTCAGTGAGGGGCACATATGGGAGCTTTGTTCAGATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaaatattaatcttattcatttgtacctttttcttataatcccttggatccagGTTTCTCCTCCTTCAGTGAGGGGCACATATGGGAGCTTTGTTCAGATTGCAACCTGCCTTGGAATCGTAGTATCTCTCCTAATTGGTACACCTGTGAAGG
      tattaat  putative branch site (score: 2)
                                         tccctt  putative PPT
     atattaatcttattca  TA-rich tract