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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagacgagcggtgctctaaattactatatcatctgtcatattgccactatacaagctatgagtggctggcaatttgatcctttttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT

Basic information

species Oryza sativa
transcript LOC_Os01g05800.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G839422_T01 (Zea mays), 3'ss of exon 7
gtgagcagacgagcggtgctctaaattactatatcatctgtcatattgccactatacaagctatgagtggctggcaatttgatccttttttt-ctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT
          |   | | ||||  || | | | |||| ||| ||| ||||| | || |   |  || |||||     | ||||   |  | | |  ||||  ||||| ||||| |||||||||||| ||||  ||||||||||||||||||||||||| || |||||||||||||||||||| ||||| ||||| ||||
--------gtggatgcttctctgtat-attctttcatttgttatagtgccaat-tatacattgcga-tggcttaacttgtgatttatggtctgccacagAGCGATGACCCATCACAGAAGAACACAATGCTCATTTTGAAATTTCTTCCATTTATGATTGGCTGGTTCTCTTTGTCAGTGCCATCAGGATTGTCTATTT

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G110063_T01 (Zea mays), 3'ss of exon 8
gtgagcagacgagcggtgctctaaattactatatcatctgtcatattgccactatacaagctatgagtggctggcaatttgatcctttttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT
          ||  | | | ||  || |   | || |  || ||  ||||| | |||| | | | |    ||    || |     |  | |    |||| |||||| || || |||||||||||||| || |||||||||||||||||||||||||| || |  ||||||||||||||||| ||||| ||||| ||||
--------gtgaatgcttccctgtat-atcctttcgttggttatgatgccaat-tacatggtttaa----cttaagatcta----tggtctggcacagAGTGATGACCCGTCACAGAAGAACACACTCCTCGTTTTGAAATTTCTTCCATTTATGATTGGCTATTTCTCTTTGTCAGTGCCATCAGGATTGTCTATTT

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 7
gtgagcagacgagcggtgctctaaattactatatcatctgtcatattgccactatacaagctatgagtggctggcaatttgatcctttttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT
                 |     ||| | | |||  ||||     || |  || |    | |             |||| | |  |||||||  |||||||||||||||||| || ||||| ||||| |||||||| || ||||||||| | ||||| || |  || ||| | || || || ||||| || || ||||
-----------------gtaaagaataagtctattttctgatcattttcttctctttttgtttcattcctagtaaaattgggtttttttttttggcagACTGATGATCCATCTCAAAAGAATACACTTCTTGTTTTCAAGTTTCTTCCACTCATGATTGGTTACTTTTCTCTATCTGTCCCATCAGGATTATCAATTT

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|29615536|gb|CB620548.1|CB620548
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
EST: gi|66920591|gb|CX107439.1|CX107439
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAAC-CACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
EST: gi|29620327|gb|CB625339.1|CB625339
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
EST: gi|58694651|gb|CK083338.1|CK083338
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
EST: gi|38482468|gb|CF966504.1|CF966504
EST:     TACTTGTTGCTTCTCAGTTTGTCTCTATGGAGATCATGAAGCCACCCCAG                         ACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA
genomic: TACTTGTTGCTTCTCAGTTTGTCTCTATGGAAATCATGAAGCCACCCCAGgtgagcagac ... ttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgccactatacaagctatgagtggctggcaatttgatcctttttttctgcagACTGATGATCCATCGCAGAAGAACACACTGCTTGTTTTGAAATTTCTTCCATTTATGATAGGGTGGTTCTCTTTGTCAGTGCCGTCAGGGTTGTCCATTT
                                 atttgat  putative branch site (score: 5)
                                  tttgatcctttttttc  CT-rich tract
                                          tttttttct  TA-rich tract