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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag

Basic information

species Oryza sativa
transcript LOC_Os06g10230.1
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM5G809695_T03 (Zea mays), 5'ss of exon 24
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag
|||||||||||||| |||||||| || ||  | || |||||||| || || ||||| || ||||| ||||| | ||| ||| | ||||||||||| |||||||||| | |    | ||||||||   |||    ||| |  | |   |   ||  ||| ||  |  |     || | ||  |      |  |  |||    || | |||                                                                           
CGGAATCTAGTCAGCCTTCAAGGGTACTCGTTGTCACCTGTTGGGAACCTCCTCTTTTATGATTATATGGAGAGTGGCAGCTTATGGGATGTTTTACATGgtaagtccaggtcccaaactcatt---cagac-aatttttttgggggt---caaggaatcatgagaacagt-ttatgaagcgaccaggaactagcaccactat-tctgc---------------------------------------------------------------------------

upper sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GLYMA06G05900.1 (Glycine max), 5'ss of exon 26
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag
 | ||||| |||||||| ||||| || ||  | ||  |    |||||||||||||| || || |||||||||||||| || || |||||| || ||||||||||||         |||  | | ||          ||    || | ||||   | ||           |  ||||  | |   |  ||| |   ||||| |   |||| |   || |  ||||||                                                          
AGAAATCTGGTCAGTCTCCAAGGCTACTCTTTGTCAACGTACGGAAATCTTCTCTTTTATGACTACATGGAAAATGGCAGTCTATGGGATCTTCTGCATGgtaagt--------tcaagccttggcttgaa--agatgctgatgtactttgttgaaaa-----------cttttctgtacaatctactatgt---acattcaaccttgcattgattta--gcaata----------------------------------------------------------

upper sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 25
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 25
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag
 ||||||| ||| |||| |||||||||||||| || |||  ||| || || |||||||| || |||||||||||||| || ||||||||| |  | ||||||||||    |||  |       || ||| | || |  ||  ||||| |   |    |  |  || ||      || ||| |  || ||  ||     |  | |  ||                                                                            
AGGAATCTGGTCTGTCTACAAGGATATTCCCTGTCCCCTTCTGGGAACCTACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaaactttc------ctgaacaatatggtgctc--tgcaagtctgatctgaaaa--aatatttatcacttaaatgggtgctaaatg-tgtgtcaagaagtgtga-------------------------------------------------------------------------

upper sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 25
lower sequence: PP1S20_166V6.1 (Physcomitrella patens), 5'ss of exon 3
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag
|| ||||| |||| ||| | ||| |  ||| | ||  |  | |||||  |||||||||| |||||||||||||||||||| || |  |||  | | || |||||   |  | | |  || ||     ||  ||| |||  |  ||  | ||| || |   |   |  || |  | |     ||     | |  ||      | | | |    | | |                                                                   
CGAAATCTCGTCACTCTGCGAGGCTTCTCCATGTCCTCCATAGGAAACTTTCTCTTCTATGATTACATGGAAAATGGAAGTCTATACGATCATCTCCACGgtaaa-acataatcctcacccaggatcca-cttgcttgggac-gctctctgctcaaatttatatatttgtctgtgtggtctgctgtgaactgaacttcaataaactcgacgttatag-------------------------------------------------------------------

upper sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 25
lower sequence: PP1S19_291V6.1 (Physcomitrella patens), 5'ss of exon 25
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacag-tttgattgtcattgcaatttgcacagaagcaccaacatgccat-tctcaaaagcatgat-atttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag
|| ||||| || | ||| |  || || ||| | ||  |  | || ||  | ||||| |||||||||||||||||||||||||| |  |||  | | || ||| |   ||     || | ||    | ||  | | |    ||||    |||| || |     | ||    || | | ||  || ||  || | ||| | |                                                                                       
CGAAATCTCGTAACTCTGCGCGGCTACTCCATGTCCTCCATCGGCAACTTCCTCTTTTACGATTACATGGAAAATGGAAGCCTGTATGATCATCTTCACGgtgatgccctgtgacctaatctaaacgcaaatctaaaatccattcttgtttg-actgttctgctaattatccgtgtgtcgtaaccaaaatgacttgccgctgcag----------------------------------------------------------------------------------

upper sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 25
lower sequence: EFJ17800 (Selaginella moellendorffii), 5'ss of exon 24
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtt-tgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag
|| ||  | || ||  |  | ||||| || |||||  | |  || || || ||||||||||| | |||||| |||||||||||||||||  |  | || ||||        || |    || ||||| || | | | | |  | | || || | |||                                                                                                                                
CGAAACTTGGTAAGCTTGTATGGATACTCGCTATCCTCGGCCGGGAACCTCCTCTTCTACGACTTCATGGACAATGGAAGCCTCTGGGACATCCTCCACGgtatagcttctcttct---tctttgcaaagctctaaatcttgtggaaactttc-cag--------------------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os06g10230.1 (Oryza sativa), 5'ss of exon 25
lower sequence: EFJ16326 (Selaginella moellendorffii), 5'ss of exon 24
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag
|| ||  | || ||  |  | ||||| || |||||  | |  || || || ||||||||||| | |||||| |||||||||||||||||  |  | || ||||  || |  ||       | ||||| || |  |  ||  |    || |      ||    | |                                                                                                                       
CGAAACTTGGTAAGCTTGTATGGATACTCGCTATCCTCGGCCGGGAACCTCCTCTTCTACGACTTCATGGACAATGGAAGCCTCTGGGACATCCTCCACGgta--tgacttctcatcttcctttgcaaagctctaacgttttcatgatcttttggaaactttccag----------------------------------------------------------------------------------------------------------------------

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|58683879|gb|CK072566.1|CK072566
EST:     TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATG                         AAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
genomic: TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccg ... attattctagAAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
EST: gi|58653167|gb|CK041847.1|CK041847
EST:     TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATG                         AAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
genomic: TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccg ... attattctagAAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
EST: gi|58666076|gb|CK054762.1|CK054762
EST:     TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATG                         AAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
genomic: TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccg ... attattctagAAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
EST: gi|58653035|gb|CK041715.1|CK041715
EST:     TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTCGCATG                         AAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
genomic: TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccg ... attattctagAAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
EST: gi|58678485|gb|CK067172.1|CK067172
EST:     TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATG                         AAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
genomic: TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccg ... attattctagAAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
EST: gi|58683527|gb|CK072214.1|CK072214
EST:     TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATG                         AAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
genomic: TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccg ... attattctagAAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
EST: gi|58686490|gb|CK075177.1|CK075177
EST:     TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATG                         AAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG
genomic: TCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccg ... attattctagAAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGAATCTAGTCAGTCTTCAAGGATATTCCCTATCTCCTGTTGGAAATCTTCTCTTCTACGATTACATGGAAAATGGAAGCCTCTGGGATGTTTTGCATGgtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG