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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcacttctgtttgctgcacattgttctgtgtttctgttgcattctttgacattcttttggtcactgtgacccagcatatctagttatctactctgaccatgctacttgttcagcatttctgctctgaatttttgtgctgttttactcctacag

Basic information

species Oryza sativa
transcript LOC_Os01g66890.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66890.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G807064_T01 (Zea mays), 5'ss of exon 5
TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcacttctgtttgctgcacattgttctgtgtttctgttgcattctttgacattcttttggtcac--tgtgacccagcatatctagttatctactctgaccatgctacttgtt-cagcatttctgctctgaatttttgtgctgttttactcctacag
|||| || ||||| || ||||||| ||| || |||||||| || ||||||||||| ||||||||||     |  || || ||| | ||||| ||||| ||||||||          || || ||| | ||| | || |    ||  |     |         |   |   | ||  |  |||||||| |      | |     |||   |  | |  ||| |    || | | | || | |     |||    | | |||
TGCCCGGCGGCTGTGCCAACTGCAGGCGGATGTGGCAGCTCCTCGAGCTGCATTCCCGCATGTGCTTCCTCCCGGACACCTGCAAGGTTCCTCTCTGCAGgtgagc----------gcggcgcatcgatctct-ttgccaaagcggtagcaaatggggagaggaagaggatatgctctggcatatcttg------atttcattcatataagatataacagaacacgtgtttttatttatcgcaaattttacgacttgcag

upper sequence: LOC_Os01g66890.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0094g00950.t01 (Vitis vinifera), 5'ss of exon 6
TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcacttctgtttgctgcacattgttctgtgtttctgttgc--attctttgacattcttttggtcactgtgacccagcatatctagttatctactctgaccatgctacttgttcagcatttctgctctgaatttttgtgctgttttactcctacag
| || || || || | | ||||||||||||| |||||||||||||| ||||| || || ||||||  || || |||   |||| | || || |||||||||| |||  | | | ||   || |||  |  ||  || |  ||    |  | ||   || || ||    |         | ||||| |  |  | || | |                                                           
TCCCCGGCGGATGTGTTCACTGCAAGCGCATGTGGCAGCTTCTTGAACTGCACTCCCGGATGTGCAGTGAACCTGATTGTTGCAAGGTCCCTCTCTGTAGgtaagc--tacagattagcgc-catcatattgaattccgattatttacacattcttatcctcttcccaaaaaaattttaacatattttttattttattttatt--------------------------------------------------------

upper sequence: LOC_Os01g66890.3 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S365_10V6.1 (Physcomitrella patens), 5'ss of exon 7
TGCCTGGTGGCTGCGCTAACTGCAAGCGCATATGGCAGCTTCTTGAGCTGCATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcacttctgtttgctgcacattgttctgtgtttctgttgcattctttgacattcttttggtcactgtgacccagcatatctagttatctactctgaccatgctacttgttcagcatttctgctctgaatttttgtgctgttttactcctacag
|| ||||||| || |   | || |||||||| ||||||||||| ||||| |||||||| |||||| |  ||  |||  ||||| | || ||||||||  ||||||   ||| | |  ||     | ||| | ||        | || ||      | ||||||  |   |      || | |  |  || |     | ||    || |                                                 
TGGCTGGTGGATGTGTGCATTGTAAGCGCATGTGGCAGCTTCTCGAGCTTCATTCTCGTATGTGCACGACAAGTGATTCTTGCAAAGTGCCCCTCTGCGGgtgagt-tttcagatacct-----tcgttgtatgaagtatgcgtatactac----tgcttttgaacgaggcacagtaggaaacatcattttgagtacagatttcgcgagg-----------------------------------------------

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|88832167|gb|CI017401.1|CI017401
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88268662|gb|CI378597.1|CI378597
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTTCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88282380|gb|CI403776.1|CI403776
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|86892962|gb|CI318869.1|CI318869
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|55438958|gb|CV732779.1|CV732779
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCGTGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88276362|gb|CI396966.1|CI396966
EST:     CATTCTCGCATTTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|88966559|gb|CI353111.1|CI353111
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
EST: gi|86853111|gb|CI324813.1|CI324813
EST:     CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAG                         GCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG
genomic: CATTCTCGCATGTGCTCTGCACTTGAAACTTGCCATGTTCCCCTCTGTAGgtgagcactt ... actcctacagGCATTTCAAGGAGAAAATGCAACATCTGAGCAGAAAGGAGGAGGCCAAGTG