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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttttattttcatatggtgcttgaatttttgaattttaaatgcattgattaccatattatctatgtctaattctttattggtcagATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAA

Basic information

species Oryza sativa
transcript LOC_Os02g47410.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47410.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G849796_T01 (Zea mays), 3'ss of exon 5
gtaaggttttattttcatatggtgcttgaatttttgaattttaaatgcattgattaccatattatctatgtctaattctttattggtcagATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAA
||  | | | ||||| ||||| ||  || || | |        |||| ||   |||| |||     ||||| || ||||||     ||||||| |||||||  || || ||||||| || ||||||||||||||||||||||||||||| ||||| || || ||| |||||| 
gtgtgttgtcattttaatatgttgactggatgtct--------aatgtatatgttacaatacatgatatgtata-ttcttt-----tcagATACTGGATGCCCTGATTATCATGAAAGATGCTGGCATTATTCATTGTGATCTAAAACCAGAAAACATCCTTATAGCTCCAAC

upper sequence: LOC_Os02g47410.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G18110.1 (Glycine max), 3'ss of exon 7
gtaaggttttattttcatatggtgcttgaatttttgaattttaaatgcattgattacca--tattatctatgtctaattctttattggtcagATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAA
||| |    | | ||  ||||    ||  | ||     ||||    |  ||| || |      | |||||| |       ||| |||   |||| ||  ||| | ||| | |  | || || ||||||||||||||||||||||| || || ||||| |||||  ||  | | | 
gtatgtcaat-tctttgtatgacctttctacttggtccttttgttggttttgttttcttatcgtaatctattttcttaaatttgttg-caagATTTTATATGGACTGGCTCTACTAAAAGAGGCTGGCATTATTCATTGTGATCTGAAGCCAGAAAACATTCTTTTATGTACGAG
















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|58607868|gb|CK035901.1|CK035901
EST:     ATAGTCTAAGAGGTTTGCAACTGAAATATGTCCGAACTTTCTCTAGACAG                         ATATTGGATGCATTGGTGGGGATGAAGGACGCTGGCATTATTCATTGTGAT
genomic: ATAGTCTAAGAGGTTTGCAACTGAAATATGTCCGAACTTTCTCTAGACAGgtaaggtttt ... tattggtcagATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGAT
EST: gi|29638402|gb|CB643411.1|CB643411
EST:     ATAGTCTAAGAGGTTTGCAACTGAAATATGTCCGAACTTTCTCTAGACAG                         ATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGAT
genomic: ATAGTCTAAGAGGTTTGCAACTGAAATATGTCCGAACTTTCTCTAGACAGgtaaggtttt ... tattggtcagATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGAT
EST: gi|58610888|gb|CK038600.1|CK038600
EST:     ATAGTCTAAGAGGTTTGCAACTGAAATATGTCCGAACTTTCTCTAGACAG                         ATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGAT
genomic: ATAGTCTAAGAGGTTTGCAACTGAAATATGTCCGAACTTTCTCTAGACAGgtaaggtttt ... tattggtcagATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGAT
EST: gi|58666776|gb|CK055462.1|CK055462
EST:     ATAGTCTAAGAGGTTTGCAACTGAAATATGTCCGAACTTTCTCTAGACAG                         ATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGAT
genomic: ATAGTCTAAGAGGTTTGCAACTGAAATATGTCCGAACTTTCTCTAGACAGgtaaggtttt ... tattggtcagATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattttaaatgcattgattaccatattatctatgtctaattctttattggtcagATATTGGATGCATTGGTTGTCATGAAGGACGCTGGCATTATTCATTGTGATCTAAAACCGGAAAATATTCTCATAACTCCAAA
                                  gtctaat  putative branch site (score: 3)
                                        ttctttatt  CT-rich tract
                                   tctaattctttatt  TA-rich tract