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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatattattctctcctcttgatatcagtacaatgttaaaattttgaacacgcatctaatctattttcactctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGG

Basic information

species Oryza sativa
transcript LOC_Os05g07070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07070.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G118344_T05 (Zea mays), 3'ss of exon 6
gtagatattattctctcctct-tgatatcagtacaatgttaaaattttgaacacgcatctaatctattttcactctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGG
||| ||  | ||   |  | | | |||      | |   | || | |||  |  | | |||||  | || || | | ||||||| |||||||||||  |||||||| ||||||||||||| |||||||  |  || ||||||||||||||||| |||||||||||||| ||||| |||||| 
gtaaatggtgttaattattttctcataattacgcgaacatgaattcttgt-cgtgtaactaatacagttgcattgtatgtagCGTTTTATGATGCTAAATCAGTTATTTATCCATGAATCGAGAGAAGATTCTGACCCTCACTGGGACATGAGGCTGGACATTGATGATATGAGTTATGAG-

upper sequence: LOC_Os05g07070.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0019g04100.t01 (Vitis vinifera), 3'ss of exon 4
----------------gtagatattattctctcctcttgatatcagtacaatgttaaaatt-ttgaacacgcatctaatctattttcactctttgtagCGGTT--TATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGG
                |   ||| || |    |    ||     |   || | || |  || || |  |    ||  || ||| |    | |   |   || |   || ||| ||||    | |    |  |||  || ||| |    || ||||   |  |||||||||| |||||||||||||||||||| |||||| 
attctggattctccttgattatagtactactgcaaagtggatgtatagcagttttcattttgttaattatatgtcgcatatatctgttatttccatgcagGCTGTCATAATGGTGGACAGCTCATCCTTGTATGGTTCCAGAAATTTGTTTGATCAGTATGGGGACATGAGGCTGGACATTGATGACATGAGTTATGAG-
















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|218487704|gb|FG958473.1|FG958473
EST:     TTCATCATTTGATGATTGAAGACAATAACTTGGGAAGATCAGCAGCTGAG                         CGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCATGAGAAGCATTC
genomic: TTCATCATTTGATGATTGAAGACAATAACTTGGGAAGATCAGCAGCTGAGgtagatatta ... ctctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTC
EST: gi|29615678|gb|CB620690.1|CB620690
EST:     TTCATCATTTGATGATTGAAGACAATAACTTGGGAAGATCAGCAGCTGAG                         CGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTC
genomic: TTCATCATTTGATGATTGAAGACAATAACTTGGGAAGATCAGCAGCTGAGgtagatatta ... ctctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTC
EST: gi|66914386|gb|CX101234.1|CX101234
EST:     TTCATCATTTGATGATTGAAGACAATAACTTGGGAAGATCAGCAGCTGAG                         CGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTC
genomic: TTCATCATTTGATGATTGAAGACAATAACTTGGGAAGATCAGCAGCTGAGgtagatatta ... ctctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTC
EST: gi|44665886|gb|CR279320.1|CR279320
EST:     TTCATCATTTGATGATTGAAGACAATAACTTGGGAAGATCAGCAGCTGAG                         CGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTC
genomic: TTCATCATTTGATGATTGAAGACAATAACTTGGGAAGATCAGCAGCTGAGgtagatatta ... ctctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtacaatgttaaaattttgaacacgcatctaatctattttcactctttgtagCGGTTTATGATGCTGGATCAGTTAGTTATCCATGAATCAAGAGAAGCATTCGATCCTCACTGGGACATGAGACTGGACATTGATGACATGAGCTATGAGG
                             atctaat  putative branch site (score: 3)
                                   tctattttcactcttt  CT-rich tract
       aatgttaaaattttga  TA-rich tract