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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttggtaaacatgatcaagatctgttcctgtgttgcagttattttatttttccctcagaataatgaaaatttatgataatataaattcaacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGATGCCCTGATCCATCTTGTGGTGCTATGGTTCTTCAGAACATGATTAATAA

Basic information

species Oryza sativa
transcript LOC_Os08g42740.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143644_T01 (Zea mays), 3'ss of exon 4
tttttggtaaacatgatca-agatctgttcctgtgttgcagttattttatttt--tccctcagaataatgaaaatttatgataatataaattcaacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGATGCCCTGATCCATCTTGTGGTGCTATGGTTCTTCAGAACATGATTAATAA
    ||||||   | |||| |   || | |   | ||     ||| | ||| |   ||  |  || |  |  ||||| ||||     || || ||  ||  ||| || ||||| ||||||||| ||| |||||||||||||||||| |||||||| ||||||||||| ||  ||||||||||||||||    ||| ||||| |
---ctggtaacatttatcatatgactatcctgattttctttgtatgtgattatatccctcctaaaaagggggaatttctgatggctcaattttaattttgtagGCTACATTAGCGCTGCAATAGGTGGTGGTCCAGGATGTTTGTCTTTGCGATGTCCTGATCCATCATGCAGTGCTATGGTTCTTCAAGGGATGGTTAATGA

upper sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 4
----tttttggtaaacatgatcaagatctgttcctgtgttgcagttattttatt-tttccctcagaataat-gaaaatttatgataatataaattcaacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGATGCCCTGATCCATCTTGTGGTGCTATGGTTCTTCAGAACATGATTAATAA
     |  || |    ||  | | ||   |    | |  ||  || ||   ||| | |||||   |||||  |  ||||| ||||    ||||    |  ||| ||| || ||||| ||||||||  ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||    ||||||||| |
agtactcctgcttgtaattgt-atgactagcctgttttctgttgt-atgcgattgtctccctgttaataagagggaatttctgatgtcttaaa----attttttagGCTACATTAGCGCTGCAATTGGTGATGGTCCAGGATGTTTGTCATTGCGATGCCCTGATCCATCTTGTAGTGCTATGGTTCTTCAAGGGATGATTAATGA
















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|58672626|gb|CK061312.1|CK061312
EST:     GATGAGTTCTGCTGGTTGTGATCATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
EST: gi|86885710|gb|CI309837.1|CI309837
EST:     CATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: CATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
EST: gi|29635023|gb|CB640032.1|CB640032
EST:     GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
EST: gi|58680866|gb|CK069553.1|CK069553
EST:     GATGAGTTCTGCTGGTTGTGATCATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
EST: gi|88312074|gb|CI580239.1|CI580239
EST:     GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
EST: gi|29622679|gb|CB627690.1|CB627690
EST:     GATGAGTTCTGCTGGTTGTGCTCATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
EST: gi|29671896|gb|CB668171.1|CB668171
EST:     GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
EST: gi|29669832|gb|CB666107.1|CB666107
EST:     GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
EST: gi|33793942|gb|CF322859.1|CF322859
EST:     GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG                         GTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT
genomic: GATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAGgtctctctct ... aacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttttccctcagaataatgaaaatttatgataatataaattcaacctttcagGTTATATTAGTGCTGCAATAAGTGATGGTCCAGGATGTTTGTCATTGCGATGCCCTGATCCATCTTGTGGTGCTATGGTTCTTCAGAACATGATTAATAA
                                               cctttc  CT-rich tract
               aataatgaaaatttat  TA-rich tract