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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtggcgcagatatacccatcatgtgcttctttctgtaatgaggatggagtttgtactatgtatagatgcatcaacatctagtttgtaaaatttatttgcttgaacttctgtgtgcagGGTCATGAGGATCGATATTCCATTTATATCCATGCATCGCGTGAAAGACCTGTACATTCTAGTTCTTTGTTTGTTGGCCGAGAGATTCATAGTGAAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 2
gtgtggcgc--agatatacccatcatgtgcttctttctgtaatgaggatggagtttgtactatgtatagatgcatcaacatctagtttgtaaaattt------atttgcttgaacttctgtgtgcagGGTCATGAGGATCGATATTCCATTTATATCCATGCATCGCGTGAAAGACCTGTACATTCTAGTTCTTTGTTTGTTGGCCGAGAGATTCATAGTGAAAAG
|||  | ||  | ||||||||||||| |  || |     |||     ||| |||||||| ||||| | | || || |  | | | ||||||| | ||       |||||| ||| |||| ||  ||||||||||| | |||||||||||| |||||||||||||| ||||||| ||||||||||||||| ||  | |||||||| || || ||||  |||||||||
gtgcagtgcttatatatacccatcatctatttttggagttaacagatatgaagtttgtattatgtct-gttgtatta-taaccattttgtaatagttcatttagtttgctcgaaattctttgcacagGGTCATGATGGTCGATATTCCATCTATATCCATGCATCTCGTGAAATACCTGTACATTCTAGCTCCCTCTTTGTTGGACGTGAAATTCGCAGTGAAAAG

upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 2
gtgtggcgca-gatatacccatcatgtgcttctttctgtaatgaggatggagtttgtactatgtata--gatgcatcaacatctagt--ttgtaaaatttatttgcttgaacttctgtgtgcagGGTCATGAGGATCGATATTCCATTTATATCCATGCATCGCGTGAAAGACCTGTACATTCTAGTTCTTTGTTTGTTGGCCGAGAGATTCATAGTGAAAAG
||||||  |   ||||||||||||| |  |  |     |||| |  ||| |||||||| ||||| |   |   ||||| ||| | ||  | ||  | ||  |||||||||| |||| ||  ||||||||||| |  |||||||| || |||||||||||||| ||||||| ||||||||||||||| ||| | |||||||| || || ||||| |||||||||
gtgtggttcttaatatacccatcatctaatattggagttaataaacatgaagtttgtattatgtctgctgtaccatcaccattttgtaatagtttatttagtttgcttgaaattctttgcacagGGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG
















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|33676569|gb|CF304808.1|CF304808
EST:     TAACACCAGGTTCATTGCCCTTTGAGAAACTATGGGAGAAATTTCTACAG                         GGTCATGAGGATCGATA
genomic: TAACACCAGGTTCATTGCCCTTTGAGAAACTATGGGAGAAATTTCTACAGgtgtggcgca ... ctgtgtgcagGGTCATGAGGATCGATA
EST: gi|29662010|gb|CB658285.1|CB658285
EST:     TAACACCAGGTTCATTGCCCTTTGAGAAACTATGGGAGAAATTTCTACAG                         GGTCATGAGGATCGATATTCCATTTATATCCATGCATCGCGTGAAAGACCT
genomic: TAACACCAGGTTCATTGCCCTTTGAGAAACTATGGGAGAAATTTCTACAGgtgtggcgca ... ctgtgtgcagGGTCATGAGGATCGATATTCCATTTATATCCATGCATCGCGTGAAAGACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatgcatcaacatctagtttgtaaaatttatttgcttgaacttctgtgtgcagGGTCATGAGGATCGATATTCCATTTATATCCATGCATCGCGTGAAAGACCTGTACATTCTAGTTCTTTGTTTGTTGGCCGAGAGATTCATAGTGAAAAG
                                          cttctgt  CT-rich tract
             atctagtttgtaaaat  TA-rich tract