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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtccgtcagtgcaagactattgcttcacaccatctgtatatctgtatttctcttctcatcttgccattaattagtcccaggagaagtatgtcttagtttcttctccttaagcttaactgtctcgttgcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGCAATAATGATCACCAGCACCATCACTGTCGTTCTTTTTAGCACTATG

Basic information

species Oryza sativa
transcript LOC_Os07g47100.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G027851_T02 (Zea mays), 3'ss of exon 11
gtcagtccgtcagtgcaagactattgcttcacaccatctgtatatctgtatttctcttctcatcttgccattaattagtcccaggagaagtatgtcttagtttcttctccttaagcttaactgtctcg-ttgcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGCAATAATGATCACCAGCACCATCACTGTCGTTCTTTTTAGCACTATG
                                            |  ||  |      ||  ||   |  |  |   |||||               |||     |||||  |   |||||| |  |  |||||| ||||||| || |||||||| || ||| ||||||||||||| || ||||||||||||||||| |||||||| || || ||||||||||||
-------------------------------------------gttcgtgctctctgccttgtccaactttgcacccgtccc------------ctctagagggatctcccaagttttaactcttcctcttgcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 13
gtcagtccgtcagtgcaagactattgcttcacaccatctgtatatctgtatttctcttctcatcttgccattaattagtcccaggagaagtatgtcttagtttcttctccttaagcttaactgtctcgttgcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGCAATAATGATCACCAGCACCATCACTGTCGTTCTTTTTAGCACTATG
              | | ||  |    | |  |  ||  || |       | ||| ||   |  |||  | | || |||| | ||   |||       || | |||    | ||   | |   |||  |  ||| ||||||| || |  || || || |||   ||     |||||||||| |||||||| |||||||||||||| || ||||| |||||  ||
--------------gtaggagcaacaatgctgattatgggttt-------tgtcttttggaaaattg--aattatcagtcactggttcagttataaccagatgctt----taaaaactgatactct--taacaaatgcagTTCACCATGTCGGGGCACACTTCACTAAGAAGCAATGCAATCATGATCACAAGCACCATCACTGTTGTGCTTTTCAGCACAGTG

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 13
gtcagtccgtcagtgcaagactattgcttcacaccatctgtatatctgtatttctcttctcatcttgccattaattagtcccaggagaagtatgtcttagtttcttctccttaagcttaactgtctcgttgcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGCAATAATGATCACCAGCACCATCACTGTCGTTCTTTTTAGCACTATG
||  |  |  || |||  || ||  | ||     | | || | |  || |||  |   | |    ||   | | |||   || |       |||  |||    ||||| ||    ||||||           || ||||||| || |  || || || |||   ||||   |||||||||| |||||||| |||||||||||||| || ||||| |||||  ||
gtaggatcaacaatgct-gattacgggtt---gtcttttggaaaattgaattattggccac----tgatttcagttaaaacctg-------atgctttaaaaacttctact----cttaac-----------aaatgcagTTCACCATGTCGGGGCACACTTCACTGCGAAGCAATGCAATCATGATCACAAGCACCATCACTGTTGTGCTTTTCAGCACAGTG

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|88577662|gb|CI674260.1|CI674260
EST:     GGGCTGGGCTGATGAGAGGAGCTGTGTCGATTGCTCTTGCTTACAATAAG                         TTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGC
genomic: GGGCTGGGCTGATGAGAGGAGCTGTGTCGATTGCTCTTGCTTACAATAAGgtcagtccgt ... gcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGC
EST: gi|27549114|gb|CA767092.2|CA767092
EST:     GGGCTGGGCTGATGAGAGGAGCTGTGTCGATTGCTCTTGCTTACAATAAG                         NTTACAAGATCTGGCCATACTCAGCTTCACGGCAATGCAATAATGATCACC
genomic: GGGCTGGGCTGATGAGAGGAGCTGTGTCGATTGCTCTTGCTTACAATAAGgtcagtccgt ... gcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGCAATAATGATCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagtatgtcttagtttcttctccttaagcttaactgtctcgttgcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGCAATAATGATCACCAGCACCATCACTGTCGTTCTTTTTAGCACTATG
                             gcttaac  putative branch site (score: 3)
           ttagttt  TA-rich tract