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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag

Basic information

species Physcomitrella patens
transcript PP1S178_72V6.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os08g42740.2 (Oryza sativa), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| ||    || || ||||| ||||| ||  |||| || || |||||||| || ||||||||||| |||||||| |||||||||||||||||||| ||||||||   |  ||    ||| ||| ||  | |  | |||     |  | | | |  |  ||||   | || |||     ||      | | | ||                                                                           
CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtccaatgtctatgcttgctgaaat--atttatgtccatattactagtgtatgtacctctcatttgttt---tctttgaacatttcag---------------------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| ||    || || || ||||| || ||| | || |||||||||||||| || |||||||| ||||| |||||||| || |||||||||||||||||||||||   |||||  || ||   |   ||  |    || |    ||||       | |  ||    |  |||||    ||     |   ||||| |                                                                          
CTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAGTTTTGCTGgta---tgtaatcataatctctctgtttatgctcttcatagcacttgc---agtctcatatggcttgtatgtacttgt-----tctatataacgcag-----------------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os09g33876.1 (Oryza sativa), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
|  |    || ||||| || ||||| ||  |||| || || || || || || ||||||||||| || ||||| || ||||| |||||||||||||||||||||| |       |   |||     || ||   || | | |  ||   |  |||| | | |   | | | |     |   |    ||   | |    ||                                                                    
CTTATTCTAAGCCCTGTCCGAAATGCAAACGACCTATAGAGAAGAATCAGGGATGCATGCATATGACATGCACTCCTCCTTGTAAATTTGAGTTTTGCTGgtaagct-------tccctctcggcatatttgttttgatggtgattgtgtacattttgcattgaaattgtttatctttggtctgattttccatggttgcag-------------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM5G876621_T02 (Zea mays), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| ||    || || || || ||||| ||  | || ||||||||||| || || |||||||| || || ||||| ||||| |||||||||||||| ||||||||||           ||||||||||||   |  |||   ||| ||| |       | |   |  |||   ||   | | | ||  |  ||  |                                                                          
CTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaagc----------attcttactttatgcattttattctta-ttagtgcttgcaaatgaaacaaattgatggctg-cgctatcttactacag--------------------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GRMZM2G006428_T01 (Zea mays), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| ||    || || || || ||||| ||| | || ||||||||||| || || |||||||| || || ||||| ||||| |||||||||||||| |||||||| |           |||||| ||||  |            | || |||    ||| || | |||  |  || ||  ||  ||  || ||   |||| |   |||                                                              
CTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAGTTCTGCTGgtaggc----------attctttcttttata----------cattttatt---cttattagttttagcaaatggaaaacatgatagttgtactatcat-actacag--------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
||||   ||| ||||| || ||||| ||  | || || || |||||||| || || ||||||||||| ||||| ||||| || ||||||||||| |||||||||||||   |||   |  ||  || |   ||||    | ||     |  ||  |  | || ||| | | |  |     || || | ||       | || |    |                                                            
CAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAGTTCTGCTGgtaagttg---ataaagtggttgattaaacaaaat----gctataatgtcagaagttatgcttttattctctctatacttcc-tg-taatctaactctgaattggattc-----------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgc--ttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| ||   ||| || || || || |||||| | || || |||||||||||||| || |||||||| || |||||||| || || |||||||||||||||||||||||| || ||| |   |||  | ||| || | | |  |   || |   | | | ||  |  |   || |   |  |||   ||     ||   | |||||                                                                   
CTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTGgtaagtt-tatatact---cttgttctagatagactcacatgtatttaggaggtctggtctttattccattttgtatccacttggcaacactagcattatcaag------------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ15174 (Selaginella moellendorffii), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaat-tggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| |||  |||||| ||||| ||||| || |||||||| ||||| |||   || |||||||| ||||| || || ||||| ||||| ||||| |||||||||||||||   | |  |||  ||   || | || ||  |   |  |||   |  ||  ||                                                                                                              
CGAACTCCAAACCATGCCCGAAATGCAAAAGACCGATAGAAAAGAACTTGGGGTGCATGCACATTACCTGTACGCCACCGTGCAAGTTTGAATTTTGCTGgtaagttcacatttctatcgtt--cttggctagatacatcatgtttaccatctatacag--------------------------------------------------------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttact--ttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| |||  |||||| ||||| ||||| || |||||||| ||||| |||   || |||||||| ||||| || || ||||| ||||| ||||| |||||||||||||||   | |  | |  ||  |   |||||| || |   ||||     |  ||  ||                                                                                                              
CGAACTCCAAACCATGCCCGAAATGCAAAAGACCGATAGAAAAGAACTTGGGGTGCATGCACATTACCTGTACGCCACCGTGCAAGTTTGACTTTTGCTGgtaagttcacatttctgtcgttcttggctagttacatcatgtttacca---tctatacag--------------------------------------------------------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ17699 (Selaginella moellendorffii), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| ||   |||||| || || || ||||| |||||||| ||||||   ||||| ||||||||||| || || || || || ||||| ||||||||||||||||| ||  |   | || ||||  ||   |    ||| | ||    ||                                                                                                                         
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgttt--tctttttctcgctgatgactgattgatgtgtggtag------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ16231 (Selaginella moellendorffii), 5'ss of exon 8
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag
| ||   |||||| || || || ||||| |||||||| ||||||   ||||| ||||||||||| || || || || || ||||| ||||||||||||||||| ||  |   | || ||||  ||   ||   ||| | ||    ||                                                                                                                         
CCAATTCCAAACCTTGTCCAAAGTGTAAAAGACCGATCGAAAAATCTCAAGGATGCATGCATATAACGTGTACGCCTCCGTGCAAGTTTGAGTTTTGCTGgtaggtgatt--tttttttctcgctgatgtctgattgatgtgtggtag------------------------------------------------------------------------------------------------------------------------

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|22132083|gb|BQ826972.1|BQ826972
EST:     GGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTG                         GCTGTGTCTTGGAGCATGGACTGATCACGGTGAACGAACTGGAGGTTTCTA
genomic: GGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgta ... tctttggcagGCTGTGTCTTGGAGCATGGACTGATCACGGTGAACGAACTGGAGGTTTCTA
EST: gi|162175945|gb|FC352351.1|FC352351
EST:     GGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTG                         GCTGTGTCTTGGAGCATGGACTGATCACGGTGAACGAACTGGAGGTTTCTA
genomic: GGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgta ... tctttggcagGCTGTGTCTTGGAGCATGGACTGATCACGGTGAACGAACTGGAGGTTTCTA