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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgagctatgccttttcttttcttttttcctcacaaaatatccacaatccaagtattagctgttttgaccttggttacatattgctttacttcctttacagGTGCAAGAGAAGAAAGTAAAACAAGTTTCAGTTATGAATTTGGATTCACGGAGTGTAGGGACTGGTACCTCTTCTAGTGCAAGTACTAGTAGTTCTAGGG

Basic information

species Oryza sativa
transcript LOC_Os06g36770.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 5
--cgagctatgccttttcttttcttttttcctcacaaaatatccacaatccaagtattagctgttttgaccttggttacatattgctttacttcctttacagGTGCAAGAGAAGAAAGTAAAACAAGTTTCAGTTATGAATTTGGA---TTCACGGAGTGTAGGGACTGGTACCTCTTCTAGTGCAAGTACTAGTAGTTCTAGGG
     |     ||  | | || | |||||  |       | |   ||||   |||  |   | ||||  | ||| ||||  ||||||||| || || ||||||| ||||||||||||||||||| | || |||| |||||||||||   ||| |  |||| ||| | | ||||| || ||| ||||||||| ||||||||||   
tatatgtggcaccactgcattgcatttttaattgtttcttctat-caattgcagt-ctgtttttttttgctttgcttactcattgctttaattactgtacagGTTCAAGAGAAGAAAGTAAAACGATTTGCAGTCATGAATTTGGACAGTTCCCAAAGTGCAGGAAGTAGTACCACTGCTATTGCAAGTACCAGTAGTTCTA---
















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|33796287|gb|CF324010.1|CF324010
EST:     ATTCACTCTCCCTTCTGTCTACAAATGATAAAACAATAAAATACTGGAAG                         GTGCAAGAGAAGAAAGTAAAACAAGTTTCAGTTATGAATTTGGATTCACGG
genomic: ATTCACTCTCCCTTCTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggagaa ... tcctttacagGTGCAAGAGAAGAAAGTAAAACAAGTTTCAGTTATGAATTTGGATTCACGG
EST: gi|58660482|gb|CK049162.1|CK049162
EST:     TCACTCTCCCTTCGTGGGCTACAAATGATAAAACAATAAAATACTGGAAG                         GTGCAAGAGAAGAAAGTAAAACAAGTTTCAGTTATGAATTTGGATTCACGG
genomic: TCACTCTCCCTTC-T-GTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggagaa ... tcctttacagGTGCAAGAGAAGAAAGTAAAACAAGTTTCAGTTATGAATTTGGATTCACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccaagtattagctgttttgaccttggttacatattgctttacttcctttacagGTGCAAGAGAAGAAAGTAAAACAAGTTTCAGTTATGAATTTGGATTCACGGAGTGTAGGGACTGGTACCTCTTCTAGTGCAAGTACTAGTAGTTCTAGGG
                ttttgac  putative branch site (score: 3)
                                   ttgctttacttccttt  putative PPT
                            ttacatatt  TA-rich tract