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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacattattcttatttatatttttcttgttttaccatatgttttcttatcgctagcatgcccattaactgcttacagtttttatcttgaaatttagGGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACCTTTTGTTAAG

Basic information

species Oryza sativa
transcript LOC_Os11g03780.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------------gtaatacattattcttatttatatttttcttgttttaccatatgttttcttatc--gctagcatgcccattaactgcttacagtttttatctt--gaaatttagGGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACCTTTTGTTAAG
                                        |  |    | || || | | | ||||| || || |     |     |  |||     |  ||||    ||   || ||     || |  |||   ||||  ||| ||||||||| ||||||||||||||||||| |  || | ||| |||||| | 
gtaagcatatgcccagtcccttgactctgtttgtaaatgtttgtgtgcttttattttctttctttttttttttctgaagaaaaaaattctattcaattgacatgttttttctttgtttttttcttgttgctttaaaaatacagGAATCAGCCACAATGATGAAGTCGATACCACTAGTATCGGACCCTTTGTTCAA
















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|33796127|gb|CF323929.1|CF323929
EST:     CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGGTTG                         GGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACCTTTTGTT
genomic: CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATG-TTGgtaatacatt ... tgaaatttagGGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACCTTTTGTT
EST: gi|33796277|gb|CF324005.1|CF324005
EST:     CTTTCTGAAGACCTGGGTGCTGCCC-TATTTTGGGGTGTTCAATGGCTG                         GGATCAGCCACCATGNATGAAGTCGATACCACCATAATTGAACCTTTTGT
genomic: CTTTCTGAAGACCTGGGTGCTGCCCCTATTT-GGG-TGTTCAATGT-TGgtaatacatt ... tgaaatttagGGATCAGCCACCATG-ATGAAGTCGATACCACCATAATTGAACCTTTTGT
EST: gi|27548162|gb|CA766165.2|CA766165
EST:     CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTG                         GGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACCTTTTGTTA
genomic: CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTGgtaatacatt ... tgaaatttagGGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACCTTTTGTTA
EST: gi|88722894|gb|CI746404.1|CI746404
EST:     CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTG                         GGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACC
genomic: CTTTCTGAAGACCTGGGTGCTGCCCCTATTTGGGTGTTCAATGTTGgtaatacatt ... tgaaatttagGGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttatcgctagcatgcccattaactgcttacagtttttatcttgaaatttagGGATCAGCCACCATGATGAAGTCGATACCACCATAATTGAACCTTTTGTTAAG
                           tgcttac  putative branch site (score: 2)
                                    tttttatctt  putative PPT
                                    tttttatcttgaaatt  TA-rich tract