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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag

Basic information

species Physcomitrella patens
transcript PP1S10_200V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os04g35700.1 (Oryza sativa), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
|| ||  ||    |     | |  |||||||| ||||| ||||||||||||||||||||||||  |        | |||  |   |   | |        || |||  | |||  | ||   | ||   || |||   |   |  |  | | ||||||                                                             
ATATCATCTTTTGCTGAAATACGCTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAGgtaaat--tgtttttctaacagtaaacctttatataccgtat-ttatcatcatctttatatgattc---tgaattctcctaatgattgtaacatgcag-------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os11g10100.1 (Oryza sativa), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgta-tgtgtcaaacgtataattgattatgctgactgtttacatcttacaa-acatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
|| || || ||  | | | || |||| ||||| |||||||||||||||||||| ||||||||| ||   || | ||  ||   | |   |||     |  ||| |||       | || |||   ||  ||||   ||  |   ||  | || |||        |                                                        
ATATCAGCGCACACATCTATCAAGTCCTTCAAAGGAAGCCCTTACTGGATGGCGCCTGAGgtaatgcaacagaagttgaaaaaactt--ctgtactctgccattttaagttggttgcttatc---attttctgttgttttctcatagaattttaattttcctcag--------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os02g35010.1 (Oryza sativa), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtg-tcaaacgtataattgattatgctgactgt-ttacatcttaca-aacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
 |  |  ||    ||    | |  |||||||  |||||||| ||||||||||||||||||||||  | |     || ||    | |  |   ||||| | | || |||   ||  ||||   ||||      |   |  | |      ||   |  |||||                                                             
GTGACATCTTTCGCCGAAATACGCTCTTTCAGAGGAAGCCCATACTGGATGGCTCCTGAGgtatacggtttcctgtttacaacacttggagcactgtgtcatatgttatgtaatttacttcaccaagaacggtttgtccaactaaatgtaaa-acgtgcag-------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 5'ss of exon 8
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||   ||  ||    | |  |   || || ||||| ||||| |||||||||||||||||||||  ||  || | || | |    ||  ||     | |  |  |     |   | | || |  ||| |||        ||| | |||   |||| ||    ||   || | | | ||          ||| || ||  |                    
ATCAATGGGCAGCAGTGTGCCTTTTCATTTAAGGGTAGCCCGTACTGGATGGCTCCTGAGgta-atgaaaatcctacattcttctacact-----tctctagttatttgatgaatttatgcctatcttctct------ccgctgttataaaaat-caaccttgcttctctcacacatgt--------aataactatgcag-------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G140726_T01 (Zea mays), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaat--cgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
|| ||  ||    |     | |  |||||||| ||||| |||||||||||||||||||||||  | |  |     |||    | |    ||| | |||        |     | |   ||  |||   ||   |   |    || |   ||| |                                                                   
ATATCATCTTTTGCTGAAATACGTTCTTTCAAAGGAAGTCCTTACTGGATGGCTCCTGAGgt--gagctattttaataccgaacttccttgattatttgtcataatctgctgtgcgtctctgaatgaagttctcccatcattgggaaaccttcag------------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G540772_T01 (Zea mays), 5'ss of exon 8
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatg-tgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaa-tcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||  |  ||  | ||    | || || || |  |||||||| ||||||||||||||||||||||| |||      |  |    |||        | |  |  | |      |||   ||   ||| | || || | |    |   |||  | |                                                                    
ATAACATCTTTAGCCGAAATACACTCATTGAGAGGAAGCCCATACTGGATGGCTCCTGAGgtatgctgttttctatcgacggcatttgaagagttttccatgtatggtttccatctccaggaaaagttgtgtgaagtccttcaa-attcttcag-------------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G093316_T01 (Zea mays), 5'ss of exon 8
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtat-gtgtcaaacgtataattgattatgctgact-gtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||   ||  ||    |  |     || || ||||| ||||| ||||||||||||||||||||||     ||||  |   |||| || ||||   |   |||  |    || |  ||   ||||  | | | ||| | |    | | | ||  | ||||||                                                             
ATCAATGGGCAGCAGTGCCCTTTCTCATTTAAGGGTAGCCCATACTGGATGGCTCCTGAGgtattaccccaaatcttgcattg-ttctgctactttagttattttggccagatttatatatcctgacc-tttgcttat----gttgtgacaaatatgcag-------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AC209208.3_FGT001 (Zea mays), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtat-gtgtcaaacgtataattgattatgctg-actgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||   ||  ||    |  |     || || ||||| ||||| |||||||||||||||||||||| |   ||||  |   |||| |   |||  | |  |||  |          ||   |||   |   | |   ||  |  |   | ||  | ||||||                                                             
ATCAATGGGCAGCAGTGCCCTTTCTCATTTAAGGGTAGCCCGTACTGGATGGCTCCTGAGgtattgccccaaatcttgcattg-tcccgctacattagttattttggttgggtttatatatcttgactttttttcttgtgttg---tgacaaatatgcag-------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA10G37730.1 (Glycine max), 5'ss of exon 9
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||  | |  ||||| | |||   ||| |||||||||| ||||||||||||||||||||||||     || ||  | |  || |  |   |   | | || || ||   |       ||||  |    ||||   ||       ||| |||   |    ||||  ||                                                     
ATAACAGGGCAATCGTGTCTATTGTCATTCAAGGGAACCCCTTACTGGATGGCTCCTGAGgt-----tctaatattttctttaa-accttttttttatatatattttgattg----catcttag--atctgtgattcagtatcattgctt---tctgatgattcag-----------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA16G30030.2 (Glycine max), 5'ss of exon 8
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||  | |  ||||| | ||     || ||||||||||||||||| |||||||||||||||||   ||| | |  | |   || |  |  ||    |||| |  || |||  |    ||||    |  | ||  ||||    |  || |||   |    |  |  ||                                                     
ATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCTTATTGGATGGCTCCTGAGgt---tgtaatattt-tctctgttagttttggtcctttatagatt-caatta----catcttggttttgtgacttta--tagctttgctt---tctgatttttcag-----------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA20G30100.2 (Glycine max), 5'ss of exon 2
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||  | |  ||||| |  |    ||| ||||||||||  |||||||||||||||||||||||     || ||  | |  || |      |     |||| || ||      ||  |     | |||    ||       | |||| | |    |    ||||  ||                                                     
ATAACAGGGCAATCGTGCCCATTGTCATTCAAGGGAACACCTTACTGGATGGCTCCTGAGgt-----tctaatattttctttaaaccttttttcttttatattttg-----attgtgtcttagatctgtggc------tcagtatcattgctttctgatgattcag-----------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA09G24970.2 (Glycine max), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||  | |  ||||| | ||     || |||||||||||||| || |||||||||||||||||           |||  |||   | || | ||| |       ||| | |   | | |   |     | ||    | |   |  || | |   |    |  |  ||                                                     
ATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAGgt----------tgtaatattttctctgtt-actttcagttctttatagattcaattacatattggttttgtgacttgatagctttgcat---tctgatttttcag-----------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA08G01880.1 (Glycine max), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||    |     || | ||     |||||||| ||||| |||||||||||||| ||||||||  |  | |    || | |  |||   |  ||| |||     || || |     |  ||   |   | | | | |    |  | | | | |||    |                                                            
ATAAGCGGGTCCTCTTGTCCATTTTCTTTCAAAGGAAGTCCTTACTGGATGGCACCTGAGgtcagaatgatttctaca-tccattcaac--actttttg----ttgcagatgc-tttgtctgtagtatattcttatctttgtcactgcctcaattacatag----------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA11G02520.1 (Glycine max), 5'ss of exon 10
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||   ||  ||||||| ||     |||||||| ||||| |||||||||||||| ||||||||  || | |    | |  |||| | |  ||    || |    ||  |   |   |  |     ||  |||  || |     ||                                                                           
ATAAGTGGGCAATCCTGTCCATTATCTTTCAAAGGAAGTCCTTACTGGATGGCACCTGAGgtcagtatgatttctttg-ttgagttttttg-taattgatgcttttgatgtaatattgtttgtgtca-ctgttttgattgtctag--------------------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA01G42960.1 (Glycine max), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaa-atcgtctgcatt-tagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||   ||  ||||||| ||     |||||||| ||||| |||||||||||||| ||||||||  || | |      |  ||  |||   ||  | |||   |  |  |  | |  | ||  || || || ||  |    ||    |||   ||                                                                    
ATAAGTGGGCAATCCTGTCCATTATCTTTCAAAGGAAGTCCTTACTGGATGGCACCTGAGgtcagtatgat-----ttctttgttaacttgcatttttttgttattgatgctt-ttgatataatattgtttgtgtcactgctttgattgtctag-------------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 5'ss of exon 7
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggta--ttacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
||  |||  || || | ||     || |||||||||||||| ||||||||||| ||||||||  |  |      | |     || |   |  || || |  | | |||| | |        |  || |     | |   | ||   |  || |                                                                    
ATCACTGGGCAGTCATGTCCTTTATCATTCAAGGGAAGCCCATACTGGATGGCACCTGAGgtcagaatgttttttcttgcc-ataaccttatctcttcatttatgacaagcttttgatagtatttcttacttctctgttcagttgttcgctcag-------------------------------------------------------------------

upper sequence: PP1S10_200V6.2 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ36960 (Selaginella moellendorffii), 5'ss of exon 6
ATTTCTGCTCAATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtcaaacgtataattgattatgctgactgtttacatcttacaaacatactcatccaaatcgtctgcatttagccggtattacttaaatgcagtgatggagctgttagagattcccctcctcaattacgatttaacatgattcttaattggcag
 | ||| ||   ||  || | |  ||||| || ||||| || ||||||||||||||||||||||||     |||| |  ||  || |    | |  ||  ||   ||   || ||   | |   |  |  |  |||     ||| | |  |||                                                                  
-TATCTTCTAGTTCACTTGTGCTATCTTTTAAAGGAAGTCCCTACTGGATGGCTCCTGAGGTATGTCC---ACGTTTTCTTTCTTCT----AATACTTCTATGACACCgtcacacggctactcctttttaggttttcaagagtaatgcgcaaag-----------------------------------------------------------------

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|162194513|gb|FC370736.1|FC370736
EST:     AATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG                         GTAATCAAGAATTCAGGAGGGTATGATTTGGCTGTGGATATATGGAGTCTA
genomic: AATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtca ... taattggcagGTAATCAAGAATTCAGGAGGGTATGATTTGGCTGTGGATATATGGAGTCTA
EST: gi|162169368|gb|FC346258.1|FC346258
EST:     AATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG                         GTAATCAAGAATTCAGGAGGGTATGATTTGGCTGTGGATATATGGAGTCTA
genomic: AATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtca ... taattggcagGTAATCAAGAATTCAGGAGGGTATGATTTGGCTGTGGATATATGGAGTCTA
EST: gi|162166784|gb|FC342961.1|FC342961
EST:     AATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG                         GTAATCAAGAATTCAGGAGGGTATGATTTGGCTGTGGATATATGGAGTCTA
genomic: AATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtca ... taattggcagGTAATCAAGAATTCAGGAGGGTATGATTTGGCTGTGGATATATGGAGTCTA
EST: gi|100449751|gb|CJ973917.1|CJ973917
EST:     AATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAG                         GTAATCAAGAATTCAGGAGGGTATGATTTGGCTGTGGATATATGGAGTCTA
genomic: AATCCTTTCTCCAGTCTTTCAAGGGAAGCCCTTACTGGATGGCTCCTGAGgtatgtgtca ... taattggcagGTAATCAAGAATTCAGGAGGGTATGATTTGGCTGTGGATATATGGAGTCTA