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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatgttcttcatctttgagaatgagtatgcaagtttccttggggttaggaggcaccataatgtgcgaatttctttggactgcttttgagagacctctcctgtgatatttccttatatgtacctgtttagtgtagGTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGAGGGCACACTGACAATATCAGGGCTTTACTTCTTGATCCTACTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os12g06810.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 6
gtattatgttcttcatctttgagaatgagtatgcaagtttccttggggttaggaggcaccataatgtgcgaatttctttggactgcttttg--agagacctctcctgtgatatttccttatatgtacctgtttagtgtagGTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGAGGGCACACTGACAATATCAGGGCTTTACTTCTTGATCCTACTGGCAG
|||||    ||||||  |   | ||| || ||| |  |||  |   | |||  || |     ||   || | ||||  |  ||   ||     | |||||| |  ||   |||||                     | ||||||| || || |||||||| ||||| || || || || |||||||||||||||||||||||||||||||| || || ||| ||||| |||| || ||
gtattgcactcttcacgtaacataataagaatg-acattttgtgatgattacaagactagtcaaca-gccagtttcagtacacattttcccctaaagaccttttttgctttattt---------------------gaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGAGGGCACACTGACAATATCAGAGCCTTGCTTGTTGATTCTACAGGGAG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S28_153V6.1 (Physcomitrella patens), 3'ss of exon 5
----gtattatgttcttcatctttgagaatgagtatgcaagtttccttggggttaggaggcaccataatgtgcgaatttctttggactgcttttgagagacctctcctgtgatatttccttatatgtacctgtttagtgtagGTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGAGGGCACACTGACAATATCAGGGCTTTACTTCTTGATCCTACTGGCAG
    ||  || |||       | |   | |    | |      | | ||    ||  |  |      || ||| || |     | | || ||| || ||  |  |       | |  ||| |  |||  |||  | ||||||||||| || ||||||||||| || ||||| || ||  |||||||| | | ||| |||||||||||| |  | ||| ||||||| || |||||||||||
gtcagttgtacgtttccagcttattttattcgaaaagtgtccattcctg--actactactctttcacatttgc-aactcgagagaagtgatttaga-agttccatttcaaattgtaacctcacctgt-tctgagtcgtgtagGTTGTCCGAGTTTGGGATCCAAGAACTGGATCTAAACAAATGAAACTAAAAGGTCACACTGACAATGTTCGAGCTCTACTTCTAGACCCTACTGGCAG

upper sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S84_74V6.1 (Physcomitrella patens), 3'ss of exon 6
gtattatgttcttcatctttgagaatgagtatgcaagtttccttggggttaggaggcaccataatgtgcgaatttctttggactgcttttgagagacctctcctgtgatatttccttatatgtacctgtttagtgtagGTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGAGGGCACACTGACAATATCAGGGCTTTACTTCTTGATCCTACTGGCAG
                                   | |||  | || | ||   |   ||||  | ||  ||| |   ||  ||     |  |    || | || |   |    || || ||  |    |   ||||||  || || || |||||||| || ||||| || ||| |||||||||| | ||| |||||||||||| |  ||||| | ||||| || |||||||||||
-----------------------------------atttttttaggtgctaattgttcccatg-tttgataatgttggtgttcttgacgtcggtctgcttttctttatcaag--ctaatttggtctgagtctctgtagGCGGTCCGAGTGTGGGATCCAAGAACTGGATCTAAGCAAATGAAATTAAAAGGTCACACTGACAATGTTCGGGCTCTCCTTCTAGACCCTACTGGCAG

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|29678630|gb|CB674905.1|CB674905
EST:     TGGCCATGAGTGACACAGGAAACACACTTGTCTCTGGTGGTACTGGAAAG                         GTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGA
genomic: TGGCCATGAGTGACACAGGAAACACACTTGTCTCTGGTGGTACTGAAAAGgtattatgtt ... tttagtgtagGTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGA
EST: gi|29670913|gb|CB667188.1|CB667188
EST:     TGGCCATGAGTGACACAGGAAACACACTTGTCTCTGGTGGTACTGAAAAG                         GTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGA
genomic: TGGCCATGAGTGACACAGGAAACACACTTGTCTCTGGTGGTACTGAAAAGgtattatgtt ... tttagtgtagGTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGA
EST: gi|117217320|gb|CT852008.1|CT852008
EST:     TGGCCATGAGTGACACAGGAAACACACTTGTCTCTGGTGGTACTGAAAAA                         GTTGTTCGCGTTTGGG
genomic: TGGCCATGAGTGACACAGGAAACACACTTGTCTCTGGTGGTACTGAAAAGgtattatgtt ... tttagtgtagGTTGTTCGCGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttttgagagacctctcctgtgatatttccttatatgtacctgtttagtgtagGTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGAGGGCACACTGACAATATCAGGGCTTTACTTCTTGATCCTACTGGCAG
                                         cctgttt  CT-rich tract
                        atatttccttatat  TA-rich tract