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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctgctgatgttttgttggccttgaactcctactctcattttgcttttgaccagaaactttgcctgaggatttcttttctagaacgataagtgtctttgatgtttgttggctttgaaattctgttgtagcttgccatatacctttctgattgctgaacttattgtcttgttctccagGGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATCATGCTTGCAGTGACATTAGTGAAACTTGCCCTTGTTTTATATTGCCGGA

Basic information

species Oryza sativa
transcript LOC_Os01g62070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62070.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G014454_T01 (Zea mays), 3'ss of exon 4
gtaagtctgctgatgttttgttggccttgaactcctactctcattttgcttttgaccagaaactttgcctgaggatttcttttctagaacgataagtgtctttgatgtttgttggctttgaaattctgttgtagcttgccatatacctttctgattgctgaacttattgtcttgttctccagGGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATCATGCTTGCAGTGACATTAGTGAAACTTGCCCTTGTTTTATATTGCCGGA
                                                                     | || | || |||  ||| || |     ||||  |    |   ||      ||||  | || | | ||||| |     ||  | ||  |  |   |  | |||  |||||||||| ||||| |||||||| ||||  || |||||||||||| ||||||||||||||||  | |||||||| || ||||||||||| ||| ||||||||||  
--------------------------------------------------------------------gttagtaatt-tttcttagtacca-----gtctaagggtctaactgt-----aaatcatattattgtttgccct---tgttgattatcacatatgatcatatctaattctccagGGAGATGAATTCAGCTTAACAAGTGATCAAGAAAAGTGGCTTGTGGACATCATGCTCTCCGTGACATTGGTAAAACTTGCCCTGGTTATATATTGCCGCT
















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|29661349|gb|CB657624.1|CB657624
EST:     CACTTGGCCTTCAGATCATCCTAGAATCAGTACGCTCGTTGTTGTCTGAT                         GGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATC
genomic: CACTTGGCCTTCAGATCATCCTAGAATCAGTACGCTCGTTGTTGTCTGATgtaagtctgc ... tgttctccagGGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATC
EST: gi|33364700|gb|BP433013.1|BP433013
EST:     CACTTGGCCTTCAGATCATCCTAGAATCAGTACGCTCGTTGTTGTCTGAT                         GGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATC
genomic: CACTTGGCCTTCAGATCATCCTAGAATCAGTACGCTCGTTGTTGTCTGATgtaagtctgc ... tgttctccagGGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATC
EST: gi|29620907|gb|CB625918.1|CB625918
EST:     AATCAGTACGCTCGTTGTTGTCTGAT                         GGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATC
genomic: AATCAGTACGCTCGTTGTTGTCTGATgtaagtctgc ... tgttctccagGGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtagcttgccatatacctttctgattgctgaacttattgtcttgttctccagGGGGATGAGTTCAGCTTGACAAAAGAGCAAGAAAAGTGGGTTGTGGACATCATGCTTGCAGTGACATTAGTGAAACTTGCCCTTGTTTTATATTGCCGGA
                     ttctgat  putative branch site (score: 3)
                                       ttgtcttgttctcc  putative PPT
                                 aacttatt  TA-rich tract