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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag

Basic information

species Physcomitrella patens
transcript PP1S7_163V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os02g09840.1 (Oryza sativa), 5'ss of exon 9
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgcta--gttaatgtgaagttttcactgaaacttatcctctactctggctgcag
 ||||  ||||||||||||||||| ||||| |||||||| ||||| ||||| || ||||| || ||| | |||||| | |  |||||||| |||||||  |||| |     |  |   | ||||  |||          ||||||   ||   || |||     |  ||   ||| ||   ||||| ||   || |  | |                          
CTTTTTTGAGGAGCAACTTCATCGCATGGAATGCATGGCCCAGGAACCTGTACTGTTTGAAGACATCTTGTGTCAACTAATTGATATGATTGGACCTGAGgtaacca----aaca--tttttctgtattt---------ctattctgttactaggttcttaggctttttaagctgatatatttaatttgttcttgtttcag--------------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctc-gcat-tcatttcactg--ctagttaatgtgaagttttca--ctgaaacttatcctctactctggctgcag---------------------
||| || ||||||||| | || ||||||||||||||||| || || ||||| ||||||||||| ||  | || || ||||  |||||||| ||||| |  |||     |||   ||  |  |  |      ||    |  | || ||  |   |  | || |||| |      | ||  | | ||||||  || ||       |  ||   |  |  ||  |||  |                         
TTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAAGAACCTGTGCTTTTTGAGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagcatcttggacagaattattgatgcattttaggcctgt-ttggaacagtggaatgtcagcatgttgaggaattgcaccatttaatgcaaaattcctgtgttccaaacaagtccttaaactgaatttgataaatcttttcttttccacag

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G080083_T01 (Zea mays), 5'ss of exon 9
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
 || |  ||||||||||||||||| |||||||||||||| ||||| |||||||| |||||||| ||| | |||||  | |  |||||||| |||||||  ||   | ||  |||| | |  |  |  |   |    |    |||  |         |   ||||| ||||   | | ||                                              
CTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAGGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgttgccttt--agtacttttgtgcatttccatgttatagacattttatgctgaatattatgcattaattttgtt-ccag----------------------------------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G040094_T01 (Zea mays), 5'ss of exon 9
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcac-tattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
 |||| |||||||||||||||||| |||||||||||||| || || |||||||| |||||||| ||| | |||||  | |  |||||||| |||||||  ||  || |||    | | | | |         |  |  || | ||   || |||  ||   ||||| || |   | | ||                                              
CTTTTTCGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAAGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATCGATATGATTGGACCTGAGgtt-gcctttattaattttgtgcattgccaagttataaacattttatgctgaattagttatgcattaatcttgtt-ccag----------------------------------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
||| |||||||||||| | || || |||||||||||||| || |||||||| ||||||  ||| ||  | || || ||||  |||||||| ||||| |  |||     |     |     |  |||||     | || |    | | ||  ||   | |    | | ||  || |                                                  
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcataca-----tattacataaac-gttttatc--tgggcttgataaatattt--tcctttctacag--------------------------------------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA20G36530.1 (Glycine max), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcatt-catttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
|||||| ||||| ||| | |||||||||||||||||||| || |||||||| ||||||||||| ||  | ||||| || |  || |||||   |||||  ||  || |||   |  |   ||  |   | |||   ||  | ||  | |   | | | |   ||  | |||  |||  |   || ||  |  | | | |||                         
TTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTTTTTGAGGACATATTGTGTCAGATAATTGACATGATTAAACCTGAGgtttgcctttccatctttcttttgatgattgtttgatctttttttcattgtgttgttgtgaaataacctttgcctggaaaagaaagtacaactct-agtga-------------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA19G43790.1 (Glycine max), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttc-tacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatg-tgaagttttcactgaaacttatcctctactctggctgcag
|||||| ||||||||| | ||||| |||||||||||||| || || ||||| ||||||||||||||  | || || || |  || ||||| |||||||  ||  |  ||| | |  | | ||  |  |||| ||||     ||||    | |   |   || ||||  ||  | |   |  |  |  |  ||| |  | |                           
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaatgttttttttatttattgtttgcccttgtattgtgttgatgagaagtcacattagttggaatatgatatgctaatctagtctgtagt---------------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
|||||| ||||||||| | ||||| |||||||||||||| || || ||||| ||||||||||||||  | || || || |  || ||||| |||||||  ||  |  ||| | |  | | || |  | || ||| ||  |  ||  | ||  | | |   | | |||  | |  ||| |  ||| |||  || |      ||  ||  |  ||            
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaatt-ttttttttctactgattgttt-gcccttgtattatgttgatga-gaagtcacatta--gctgg--aatatgatattct------aatctagtcagta------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA10G30930.1 (Glycine max), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
|||||| ||||||||| | ||||||||||| |||||||| || |||||||| || |||||||| ||  | ||||| || |  || |||||   |||||  ||  || |||   || |   ||  |   || ||| || |   ||| |  |    ||| | | |   | ||    |  |  | |  | ||   || |  |                          
TTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAAGAGCCTGTGCTCTTTGAGGACATATTGTGTCAGATAATTGACATGATTAAACCTGAGgtttgcctttccatatttcttttga---tgattgtttgatc-ttctatcattgtggtgttgtaa--aattgttggacaagtgacctcaataatttaaggggggggg-------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA10G32500.1 (Glycine max), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
 ||||| ||||||||  | |||||||||||||||||||| || |||||||| || ||||| |||||  | ||||| ||    |||||||| ||||| |  ||     ||||       ||||     ||| ||  || |||  |    |   |      | |     | |  |   | || | |||      ||  | |                          
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtt--tttgttttactcctctgcagtatagcaagtggtaactgtcctacgtttgcag--------------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
 ||||| ||||||||  | |||||||||||||||||||| || |||||||| || ||||| |||||  | ||||| ||    |||||||| ||||| |  ||     ||||       ||||     ||| ||  || |||  |    |   |   |  | |     | |  |   | || | |||      ||  | |                          
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttgcgtcttgattcttttacttgtt--tttgtttcattcctctgcagtatagcaagtggtaactgtcctacgtttgcag--------------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgt--aagcgtttgagtagtctcttctacattggttgcttcac-tattcgactaaatgggtctcgcattca-tttcactgctagttaatgtga---agttttcactgaaacttatcctctactctggctgcag
 ||||| || |||||  | ||| | |||||||||||||| || ||| |||||||||| ||||||||| | ||||| ||||  ||||||||||||||||  ||  ||   | |   |  | | |||| | ||   |  ||    || ||    || | | |   |    || |||   | ||   |  |||||    |||||   |   | |  |  |    ||   |  |||
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatatctcttgttttcttctttctatatttagtatagtcacagaagtagtttgtgttcccagttttctttctgagtcttgtgattttgttttgtgtttgattgttttttatttccttccacag

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 5'ss of exon 9
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgt------aagcgt---ttgagtagtctcttctacatt--ggttgcttcactat--tcgactaaatgggtctcgcattca--tttcactgctagttaatgtgaagttttcac---tgaaacttatcctctactctggctgcag
 ||||| || |||||  | ||| | |||||||||||||| || ||| |||||||||| ||||||||| | ||||| ||||  ||||||||||||||||  ||      |   ||   |||  |  |   ||||| |||  ||  | |  |  |   ||    || | | |   |    ||  |||   | ||   |  || ||  || ||     |   | |  |  |    ||   |  |||
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatgtctcttgtttttttctttctatattaaggaagatatatgacagtcacagaagtagtttgggttcccagtttttctttctgactcttgcgattttgtcttgtgtttgattgttttttatttccttccacag

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 5'ss of exon 11
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcac-tattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
 ||||| ||||||||| | ||||| ||||| |||||||| || |||||||| || |||||||||||| | ||||| ||    || ||||| | ||| |  || |  | ||        | |  |||   | |    || | | ||| | ||  | |   |  |  ||||||         | |  |     ||||  ||   |                       
CTTTTATGAGGAGCAATTGCATCGAATGGAATGCATGGCCCAAGAGCCTGTACTATTTGAGGATATCTTATGTCAGATAGTTGACATGATTGCACCAGAGgtcacggctt-------ttttcgtacccagatcatctcccgtgttctagtagttagcaataac--tcattt---------tcagggcatgatttttgcttgcag----------------------

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 5'ss of exon 7
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgctt---cactattcgactaaatgggtctcgcatt-catttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
 ||||| ||||||||  | ||||| ||||| |||||||| || |||||||| || |||||||||||  | ||||| ||    |||||||| || || |  |||  |  |   || || || | ||   |  | | ||    ||  ||   || | ||  | |    ||   |||    || ||  ||    ||                                    
CTTTTATGAGGAGCAGTTGCATCGAATGGAATGCATGGCCCAAGAGCCTGTGCTCTTTGAGGATATATTGTGTCAGATAGTTGATATGATTGGTCCAGAGgtagaccctcttgttgtttcatttattgtaatagattagtgacattttcccttactgtattttatgttgtgtttggaagcaagccaagaaaaaacgactt-----------------------------

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|162155853|gb|FC332402.1|FC332402
EST:     TTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCT                         AATGAAGGACGGTTGACACTTCGGGACTTAAAGCGATGCANATTATCT
genomic: TTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgttt ... ctggctgcagAATGAAGGACGGTTGACACTTCGGGACTTAAAGCGATGCAAATTATCT
EST: gi|162261177|gb|FC437506.1|FC437506
EST:     TTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCT                         AATGAAGGACGGTTGACACTTCGGGACTTAAAGCGATGCAAATTATCTGGA
genomic: TTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgttt ... ctggctgcagAATGAAGGACGGTTGACACTTCGGGACTTAAAGCGATGCAAATTATCTGGA
EST: gi|18334323|gb|BJ166340.1|BJ166340
EST:     TTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCT                         AATGAAGGACGGTTGACACTTCGGGACTTAAAGCGATGCAAATTATCTGGA
genomic: TTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgttt ... ctggctgcagAATGAAGGACGGTTGACACTTCGGGACTTAAAGCGATGCAAATTATCTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT