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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacacgttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag

Basic information

species Physcomitrella patens
transcript PP1S72_57V6.4
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S72_57V6.7 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G445100_T01 (Zea mays), 5'ss of exon 6
CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacacgttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag
  | ||||| ||     || || |    ||| |    || ||||| |||  |||||||||||| |||||||| ||||||||||| |||||   |||        ||     ||  |||| |  ||| | | | || |||   | | ||    |      ||| ||| | ||   ||  ||  |      | |     || ||                                                                                    
GGTCTATGGAGAACCCATTTCTGTGAAGGAATTGGCAGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatttcaagagtagtggcccata-actactggagc-atg-actttcattcatcaaactttatttt-tggttactgctcaa---ctctaaattggtttctgt---tgcatcag-----------------------------------------------------------------------------------

upper sequence: PP1S72_57V6.7 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G008623_T02 (Zea mays), 5'ss of exon 5
-------------CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacacgttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag
               | ||||| ||     ||||| |    ||| |   ||| ||||| |||  |||||||||||| |||||||| ||||||||||| |||||   | |   |||  ||  |||||  |||     ||  | | | ||  ||   | |  ||   ||    |   | |  | || |    |  | |      | |||                                                                                            
TTTAATGGACTAGGGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatattcaacagtgtccataata-actgg---aggcatg-acttgtattcatcaagcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag-----------------------------------------------------------------------------------------

upper sequence: PP1S72_57V6.7 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G130398_T01 (Zea mays), 5'ss of exon 6
CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacac-gttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag
  | ||||| ||     || || |    ||| |   ||| ||||| |||  |||||||||||| |||||||| ||||||||||| |||||   | | | |||    |  |     | || |  ||  | | ||||  ||     | ||||  ||    ||  |   ||  |  ||      |||   |   ||  |                                                                                           
GGTCTATGGAGAACCCATTTCTGTGAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatttaacagtagtggtccatgattactggaggcatg-atttgtatcgaccaaacactattttggccactgtagtaaaccctaacttggcttctcttgatcag-------------------------------------------------------------------------------------------

upper sequence: PP1S72_57V6.7 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 6
CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacacgttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag
  | ||||| ||     ||||| |    ||| |   ||| ||||| |||  |||||||||||| |||||||| ||||||||||| |||||   | |   |||  ||  |||||  |||     ||  | | | ||  ||   | |  ||   ||    |   | |  | || |    |  | |      | |||                                                                                            
GGTCTATGGAGAACCCATTCCTGTTAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatattcaacagtgtccataata-actgg---aggcatg-acttgtattcatcaagcattatcctggctactgtagtcaaccctaactcggtttctgttgtaccag-----------------------------------------------------------------------------------------

upper sequence: PP1S72_57V6.7 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G028346_T01 (Zea mays), 5'ss of exon 4
CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAA-CGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacacgttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag
  | ||||| ||     ||||| | | || | || |   | ||||| |||  |||||||||||| |||||||| ||||||||||| |||||   |||   |||    |  |     ||||   | | | |||   | |      ||| ||      ||   ||| | | | |   || |||||||| |  ||    |  | | ||  || ||   | |  |||                                                                
GGTCTATGGAGAACCCATTCCTGT-GAAGGATTTGGCAGATCGTGTAGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatattt-caacagtactggtccataacta--ctggaggcgtgacttc------tattcat-caggcattatttttttgttactgct-caagctcaaccctaagtcctaatc-tggtttctg--ttatatcag----------------------------------------------------------------

upper sequence: PP1S72_57V6.7 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G130398_T02 (Zea mays), 5'ss of exon 6
------CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacac-gttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag
        | ||||| ||     || || |    ||| |   ||| ||||| |||  |||||||||||| |||||||| ||||||||||| |||||   | | | |||    |  |     | || |  ||  | | ||||  ||     | ||||  ||    ||  |   ||  |  ||      |||   |   ||  |                                                                                           
GACCAGGGTCTATGGAGAACCCATTTCTGTGAAGGAATTGGCTGATCGTGTGGCAAGTTATGTTCATCTTTGCACGCTGTACTGGTGGCTCAGgtaatatatttaacagtagtggtccatgattactggaggcatg-atttgtatcgaccaaacactattttggccactgtagtaaaccctaacttggcttctcttgatcag-------------------------------------------------------------------------------------------

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|18335635|gb|BJ167655.1|BJ167655
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|37840289|gb|BJ598297.1|BJ598297
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208346631|gb|DC916897.1|DC916897
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|37844839|gb|BJ602847.1|BJ602847
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208367520|gb|DC954952.1|DC954952
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|67569820|gb|BJ942644.1|BJ942644
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|67693091|gb|BJ953324.1|BJ953324
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|37823229|gb|BJ581295.1|BJ581295
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|18327364|gb|BJ159366.1|BJ159366
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCT
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCT
EST: gi|162272069|gb|FC447863.1|FC447863
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|100443924|gb|BY982152.1|BY982152
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|162272070|gb|FC447864.1|FC447864
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|162267459|gb|FC444210.1|FC444210
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208371637|gb|DC932466.1|DC932466
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208369160|gb|DC956035.1|DC956035
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|37823184|gb|BJ581250.1|BJ581250
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208394276|gb|DC904096.1|DC904096
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAAGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208390148|gb|DC941955.1|DC941955
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208374326|gb|DC948386.1|DC948386
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208363378|gb|DC946976.1|DC946976
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208399219|gb|DC916574.1|DC916574
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|162209436|gb|FC386069.1|FC386069
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|37847181|gb|BJ605189.1|BJ605189
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTCACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208349231|gb|DC917995.1|DC917995
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAAGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|208357921|gb|DC943047.1|DC943047
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA
EST: gi|18366790|gb|BJ198869.1|BJ198869
EST:     GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAG                         ACCTTTTGGTTCTTCAGCTATCCTTGGAGGTCACGATCGTGATGGTCCTCA
genomic: GAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtacctttta ... tcttgttcagACCTTTTGGTTCTTCAGCTATCCTTGGAGGTTACGATCGTGATGGTCCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTATGGTGAGGAGGTTCCTATCGGAGAACTTTGTGAACGTGTTGCACATTATGTTCATCTGTGCACGCTCTACTGGTGGCTGAGgtaccttttatgacacggttaataatgtactaatttagcgacgtatttacataagttatacacgttcacaccgtttctgtttaatctctgcaagctcagcagtatacgcacaccatgacttttgaacttttgcagtagtcgtgctaaatatgtttttttcttttttcttttttcttttttctttttttttcttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG