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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgcacctctctgcttttgcacgtatactacgttagtatgtgcccggtgatttaagaatcatttttatcgtactgtttacgcgtggtgggttctgcga...

Basic information

species Physcomitrella patens
transcript PP1S26_92V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os05g36090.1 (Oryza sativa), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgcacctctctg-cttttgcacgtatactacgttagtatgtgcccggtgatttaagaatcatttttatcgtactgtttacgcgtggtgggttctgcga
| |||| || || || || ||||| ||||| || |||||||||||||| ||    || |||||||||||||||||||||||||| |||||||| || ||||||   |  |||||| ||  |  |  |||   |  ||           | |||  | |  |  ||  ||| | |  |   |     | |     |  | | 
GATTTACCGGCCCCCTCGGTGTTCGCACTGTTCAATATGCAACAATTGTGTCGAGCGCTTTGATCATCATTGCCCTTGGGTTGGACAATGCATTGGACAGgtaca-atttctctgtctgctaaagctatttcagctttcatgaaaattgatgagctcaacagaatcattaacttgttacatttatcttgacaccttagagg

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os01g64810.2 (Oryza sativa), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgcacctctctgcttttgcacgtatactacgttagtatgtgcccggtgatttaagaatcatttttatcgtactgtttacgc-gtggtgggttctgcga---------
| ||| ||| || || || ||||| ||||| ||||| ||||||||||||||   ||| ||||| ||||||||||| ||||| ||||||||||| ||  |||||   || |      ||||    || |  || | |||||  |     ||  |   |  || | | |||   ||| |   |  | |     | ||     |         
GGTTTTTCGGCCTCCTCGGTGTTCGCACTGTTCCATTTGCAACAATTGCGTGGAACGGTTTGACCATCATTGCCCCTGGGTAGGGCAATGCATTGGAAAGgta---actt------ttttttgtgtgttataagctagta-atattaagtagtgagatgattactcttacactacagcaaattcagcaactgcttgattaaaatctaaag

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G163717_T04 (Zea mays), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgt-----atgc--acctctctgcttttgcacgtatactacgttagtatgtgcccgg-----------tgatttaagaatcatttttatcgtactgtttacgcgtggtgggttctgcga----------
| | || || || || || || || |||||||||| |||  | || || ||    || ||||||||||| |||||||||||||||||||| || ||  ||||     |||   |  ||| |  |||  ||     |  | ||||     |                   |  | | |    ||  |||    | ||  | || |    |  ||||             
GATATACCGGCCTCCTCGGTGCTCGCACTGCTCCAAATGTGATAACTGTGTCGAGCGCTTTGATCATCACTGCCCTTGGGTTGGGCAATGTATTGGAGAGgttggtaatgttgatttctttattttctcagaggaaacaagttatcgattcattaaaaaaacaaatacaacctgacagctgttcctataaatcagtccaggcttatctgcatctgttttcctttgcag

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G100641_T01 (Zea mays), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgcacctctctgcttttgcacgtatactacgt-tagtatgtg-cccggtgatttaagaatcatttttatcgtactg--tttacgcgtggtgggttctgcga
| ||||||| || || || || || ||||| || |||||||||||||| ||    || ||||| ||||||||||| |||||||| |||||||| || ||||||   |   || |   | | |    ||    ||| |  | | ||    | || | ||  ||  |          |  |    |   | || ||  |||     
GATTTATCGGCCTCCTCGATGCTCACACTGTTCGATATGCAACAATTGTGTAGAGCGCTTTGACCATCATTGCCCCTGGGTTGGACAATGCATTGGGCAGgtagatagtcctatttctctactgtaatctagcgtattttttatgatttgttgctgtatcaactagcaaacataaatagaccctgaacatgttgatttca----

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA16G27910.1 (Glycine max), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatg-cacct--ctctgcttttgcacgt-atactacgttag------tatgtgcccggtgatttaagaat-----catttttatcgta--ctgtttacgcgtg-gtgggttctgcga-------
||| |||||||| || |||||||| || |||||||| ||||||||||| |||  ||| |||||||| |||||||||||||| || ||||| || || | ||||||  |  |  |  ||    ||  | | ||  || | ||       | |  |   | || |    |  |     | | ||| | |||   | ||||   ||   ||| || | | |       
GCTCTATCGTCCTCCTCGTTGTTCACATTGCTCCATTTGCAACAATTGTGTTGAACGTTTTGATCACCATTGCCCTTGGGTGGGCCAATGTATTGGGCTGgtatgatagttggcattgaccatgttcttgatgttatgataactgctttgttcgattgatgttcctggcttgctcacgtgtttcttgtaatttatttatttgtttatggcttttccaatttgcag

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA02G08790.1 (Glycine max), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgta--------tgcacct-ctctgcttttgcacgtatactacgttagtatgtgcccggtgatttaagaat-----catttttatcgta--ctgtttacgcgtg-gtgggttctgcga-------
||| |||||||| || |||||||| || |||||||| ||||||||||| |||  ||| |||||||| |||||||||||||| || ||||| || || | ||||        ||||    |  || | |||    |||  ||  |   | |      | || |    |  |     | | ||| | |||   | ||||   ||   ||| || | | |       
GCTGTATCGTCCTCCTCGTTGTTCGCATTGCTCCATTTGCAACAATTGTGTTGAACGTTTTGATCACCATTGCCCTTGGGTGGGCCAATGTATTGGGCTGgtacgatagtttgcattgaccatgttcttgatgttatgataactgctttttcaattgatgttcctggcttgtttacgtgtttcttgtaatttatttatttgtttatggcttttccaatttgcag

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA20G30860.1 (Glycine max), 5'ss of exon 2
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatg-cacctctctgcttttgcacgt---atactacgtta-gtatgtgcccggtgatttaagaatcattttta-tcgtactgtttacgcgtggtgggttctgcga----------------
| | |||||||| || ||||| || || |||||||| |||||||| || |||   || |||||||| |||||||||||||| || |||||||| || | ||||||  |  |  | |   |  ||      ||  || | ||    | | |    | |||   | ||  | |||| | ||  | |||   |        || || |                 
GTTGTATCGTCCTCCTCGTTGCTCGCATTGCTCCATTTGCAACAACTGTGTTGAGCGTTTTGATCACCATTGCCCTTGGGTGGGCCAATGCATTGGTCTGgtatgatagttgacagtcatgacatacttgattttatgatacacgttttcttctttattggtgtatgctatttacttgttttctttgttctcacgtatttttgtgccttttccaatgtgcag

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA10G36730.1 (Glycine max), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatg-cacctctctgcttttgcacgtatactacgttagtatgtgcccggtg-atttaagaatcattttta-tcgtactgtttacgcgtggtgggttctgcga----------------
| | |||||||| || ||||| || || |||||||| |||||||| || |||   || |||||||| |||||||||||||| || |||||||| || | ||||||  |  |  | |   |  || |  |  |   |   | | |  |   |  ||| | | ||  | |||| | ||  | |||   | |      || || |                 
GTTGTATCGTCCTCCTCGTTGCTCGCATTGCTCCATTTGCAACAACTGTGTTGAGCGTTTTGATCACCATTGCCCTTGGGTGGGCCAATGCATTGGTCTGgtatgatagttgacagtcatgacatgattttttgatacatgtttttcttctttattgatgtatgctatttacttgttttctttgttcttatgtatttttgtgccttttccaatgtgcag

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G24630.1 (Arabidopsis thaliana), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgcac---------ctctctgcttttgca---cgtatactacgttagtatgtgcccggtgatttaagaatcatttttatcgtactgtt-tacgcgtggt-gggttctgcga----------------------------------------------------------------------------
||||||  | || || || || || || ||||||||||||||||| || |||   || ||||||||||||||||| ||||| || |||||||| || | |||| || |         |    ||  |||| |     || | | ||| | | | |  |     |   |||  | |  ||| |  | ||||| |  |   ||    | ||||                                                                               
GCTTTACAGGCCTCCTCGCTGCTCTCATTGCTCCATATGCAACAACTGTGTTGAGCGCTTTGATCATCATTGCCCATGGGTGGGACAATGCATTGGACTGgtaagctcaatcaaaagcatattgactttgaaaaatataaagttcgtaaatttttatctcccaaaa-aagtgtgaggtttctgtttctgttatctgaaaggccaagatctgttttatctgccgattggccaatctgttgtctgccattttgtcctgtgattctgactgggaaagttctgtccattggcag

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G50020.1 (Arabidopsis thaliana), 5'ss of exon 3
---------------------GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgcacctctctgcttttgcacgtatactacgttagtatgtgcccggtgatttaagaatcatttttatcgtactgtttacgcgtggtgggttctgcga
                     ||||||||| || || || || ||||| || ||||| |||||||| || |||   || ||||||||||||||||||||||| || |||||||| ||   |||| ||       || ||    | | ||| ||   | | | |      |   || |  | |  || | | |  |      |   |||  || ||      
TAAATATTGTGATACATGCATGCTTTATCGGCCTCCTCGATGCTCCCATTGTTCCATTTGCAACAACTGTGTTGAGCGCTTTGATCATCATTGCCCTTGGgtaggccaatgcattggagtggtaagc-------tgattcaaaa-gcatattaaactgggaagatat--gcagttcataagttcttataagcagaa-----aaatgtgcaggatt------

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G50020.2 (Arabidopsis thaliana), 5'ss of exon 4
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgc--acctctctgctt------ttgcacgtatactacgttagtatgtgcccggtgatttaagaatcatttttatcgtactgtttacgcgtggtgggttctgcga---------------------------------------------------------------------------------
||||||||| || || || || ||||| || ||||| |||||||| || |||   || ||||||||||||||||||||||| || |||||||| ||   |||| ||  |       || |       ||     |||    |||  || || |    | |    | ||   |        | || |  | |  |      || || |                                                                                  
GCTTTATCGGCCTCCTCGATGCTCCCATTGTTCCATTTGCAACAACTGTGTTGAGCGCTTTGATCATCATTGCCCTTGGGTAGGCCAATGCATTGGAGTGgtaagctgattcaaaagcatattaaactgggaagatatgcagttcataagttctta-taagcagaaaaatgtgcaggattttctataaaaggatttcatattttgaggatctggtttttctagttgttgacaaaactgtgaactttaattttccatcttgacattttgttttgtgtgtgttgtgggcag

upper sequence: PP1S26_92V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv07s0031g01960.t01 (Vitis vinifera), 5'ss of exon 3
GCTTTATCGTCCACCCCGTTGTTCCCACTGCTCCATATGCAACAATTGCGTTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgcacctctctgcttttgcacgtatactacgttagtatgtgcccggtgatttaagaatcatttttatcgtactgtttacgcgtggtgggttctgcga-
| | |||||||| || ||||| || || ||||||||||| || ||||| ||    ||||||||||| |||||||||||||| || |||||||| ||   |||||||     |      |||||  | | ||   ||  | |    |   ||  ||     |  ||||| |  | || |||  |  | |     |||  |  
GTTATATCGTCCTCCTCGTTGCTCACATTGCTCCATATGTAATAATTGTGTGGAGCGATTTGATCACCATTGCCCTTGGGTGGGCCAATGCATTGGAATGgtatgctttcttggatgcttgcaactctccttacttcttttagcacatttggcttccttttttttttttttct-ctttttctgttttggaaaatctaagtt

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|162161674|gb|FC339089.1|FC339089
EST:     TTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAG                         AGAAACTATCGATTCTTTTTCATGTTCGTGTCTTCGACTTTGTTACTATGT
genomic: TTCTACGATTTGATCATCATTGCCCTTGGGTTGGGCAATGCATCGGCCAGgtatgcacct ... ttgtacgcagAGAAACTATCGATTCTTTTTCATGTTCGTGTCTTCGACTTTGTTACTATGT