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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGAGTCTTGATGAAATCAAGCTTCTCAAGTATATCAACAAGCACGACCCTGGTGACAAGCACCATCTCTTGCGGCTGTACGACTACTTTTACCACCGGgtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtag

Basic information

species Physcomitrella patens
transcript PP1S381_39V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 5'ss of exon 3
TCAGAGTCTTGATGAAATCAAGCTTCTCAAGTATATCAACAAGCACGACCCTGGTGACAAGCACCATCTCTTGCGGCTGTACGACTACTTTTACCACCGGgtaattagggtggccttt-ttgttgcatgtctttgagccatgcggacttctctgtactgtagaaag---tgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtag
 ||||| ||||||||||||||||| || |||||| |||||||||| ||||||| ||||||| ||||||| || || |||||||| ||||| ||  | ||||||| || | |    | |  |  | ||   ||||    | |   | | | |   | |  || ||||   | | | ||   | |   |||  | |     | | |                                                                                        
CCAGAGCCTTGATGAAATCAAGCTCCTGAAGTATGTCAACAAGCATGACCCTGCTGACAAGTACCATCTTTTACGTCTGTACGATTACTTCTATTATCGGgtaaatatgatattttgtgctccttcaaaccttt----cttattgtcatttagttcccatataaagcttttagtttatcacaagacatatttataaatatacaa----------------------------------------------------------------------------------------

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G181002_T01 (Zea mays), 5'ss of exon 3
TCAGAGTCTTGATGAAATCAAGCTTCTCAAGTATATCAACAAGCACGACCCTGGTGACAAGCACCATCTCTTGCGGCTGTACGACTACTTTTACCACCGGgtaa--ttagggtggcctttttgttgcat-gtctttgagccatgcg-gacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtag
 ||||| |||||||| ||||||||||| |||||| | |||||||| || |||||||||||| |||| || ||||| ||||| || ||||| ||| | |||||||  ||  | |     | ||| |  ||  | ||| ||   |     | ||  ||  ||||| |||  ||     || ||   |  |    |  || ||                                                                                            
CCAGAGCCTTGATGAGATCAAGCTTCTGAAGTATGTTAACAAGCATGATCCTGGTGACAAGTACCACCTTTTGCGTCTGTATGATTACTTCTACTATCGGgtaagtttgagcttttactcttgatagatcatttttcagtgttatttaattttgctcaactgttgaatttgtcacaactccactgcttgctggcatgtgt--------------------------------------------------------------------------------------------

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G015073_T01 (Zea mays), 5'ss of exon 3
TCAGAGTCTTGATGAAATCAAGCTTCTCAAGTATATCAACAAGCACGACCCTGGTGACAAGCACCATCTCTTGCGGCTGTACGACTACTTTTACCACCGGgtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtag
||| ||||||||||| ||||||||||| |||||| | |||||||| || || | ||||||  |||| || ||||| ||||| || ||||| ||| | ||||||| |  |      |  |  | | |  || ||   |  ||     |  | |  | |  |     ||||| ||   | || |    |||  |||   |  || |                                                                                    
TCAAAGTCTTGATGAGATCAAGCTTCTGAAGTATGTTAACAAGCATGATCCAGCTGACAAATACCACCTTTTGCGTCTGTATGATTACTTCTACTATCGGgtaaatttgagcttttactattggtagatcctttttcagtgttatttaatttcgatt--aagtgttgaatttatcacaacttc--actgcttgctgacatgtgt------------------------------------------------------------------------------------

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 5'ss of exon 4
TCAGAGTCTTGATGAAATCAAGCTTCTCAAGTATATCAACAAGCACGACCCTGGTGACAAGCACCATCTCTTGCGGCTGTACGACTACTTTTACCACCGGgtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtt-tatataggtaagcgctaaatattggtggtggtgattgtag
||| || |||||||| ||||| |||||||||||| ||||| |||| || |||| ||||||  | |||||| | || ||||| |||||||| |||  |||||||| |||  | |        ||| || | |||   |  | |         || |   |     |     || |    | ||||   |      || ||| |  ||  ||         || | |  |  |      |||| |||  | |   ||  |     || | | |||  |             
TCAAAGCCTTGATGAGATCAAACTTCTCAAGTATGTCAACCAGCATGATCCTGCTGACAAATATCATCTCCTTCGACTGTATGACTACTTCTACTTCCGGgtaagtaga-tagatgcagaattgtatcttttt---cttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaat-----tgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcag-------------

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 5'ss of exon 3
TCAGAGTCTTGATGAAATCAAGCTTCTCAAGTATATCAACAAGCACGACCCTGGTGACAAGCACCATCTCTTGCGGCTGTACGACTACTTTTACCACCGGgtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtaga-aagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttg---tggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtag
 ||||||||||| || || || ||| | |||||| |||||||||| || |||| ||||||  |||||||  | ||| |||| || ||||||||| ||||||||| |  | |  | |   | |||||    ||   |   |||    | || | ||    |    |   | |||     |   |  | |  | |  |  | ||| ||      | ||     |   | |   | | ||   || |  || ||  ||        |      ||        || |  ||| ||
CCAGAGTCTTGACGAGATAAAACTTTTGAAGTATGTCAACAAGCATGATCCTGCTGACAAATACCATCTTCTACGGTTGTATGATTACTTTTACTACCGGgtaagt--gattacatcccttttgcaaaattt--ggttttgc----tactgtatatcaaaagtgaccaattgtgtctttctcttcaacaattttagcacaagtgtgaaccatatgccttttatttaatacctttgcaatatttctctttgtggattgtttggtgtaacggattccctgaatgttctttgcag

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|162242877|gb|FC415307.1|FC415307
EST:     CTACTTTTACCACCGG                         GAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTT
genomic: CTACTTTTACCACCGGgtaattaggg ... gtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTT