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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtgatcactttttccactaaagtcttcttttacaagagatgtttagaaaatttattttggggattttgcgtatattgttttgcgcatctttctcaccatgagagttttcccgtggttttgcag

Basic information

species Physcomitrella patens
transcript PP1S9_47V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_47V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 10
GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtgatcactttttccactaaagtcttcttttacaagagatgtttagaaaatttattttggggattttgcgtatattgttttgcgc-atctttctcaccatgagagttttcccgtggttttgcag
          ||| ||||| |||||  |||| || ||| | ||| |   ||| || ||||| ||||| || || |||||||||||||||||||||||||||||| | |  || |   | ||    |     |      ||  |    |     | ||||    |  ||    |  | |||||  | || ||   ||                            
----------GTCGAGCATCTTCGACGCCAAGGCTGGAATTGCTCTTAACGATAACTTTGTCAAGCTTGTCGCCTGGTACGACAACGAGTGGGGTTACAGgtgagc-cacttgcagttcaaactattaaccatgtacaatactcc--atgcccaatttgctcttactgatctttcttttttgaactattttctgcag---------------------------

upper sequence: PP1S9_47V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G176307_T01 (Zea mays), 5'ss of exon 11
GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtga--tcactttttccactaaagtcttcttttacaagagatgtttagaaaatttattttggggattttgcgtatattgttttgcgcatctttctcaccatgagagttttcccgtggttttgcag
          ||| ||||| || ||| | || || ||  | || |||  ||  || || |||||||||||  | |||||||||||||||||||| ||||||| |  |  ||  || |  | |    || | | ||            ||    ||    || | | ||      |    || |  |  |||||                                
----------GTCTAGCATCTTTGATGCTAAGGCTGGCATTGCCTTGAACGGCAACTTCGTGAAGCTCGTGTCCTGGTACGACAACGAGTGGGGATACAGgttagttggctagttgccttcaccgattatctgactctgaccaggaggagggctt---ctgcgcacttcaaaatttaatttctatgtctcttttcag----------------------------

upper sequence: PP1S9_47V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G071630_T01 (Zea mays), 5'ss of exon 11
GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtgatcactttttccactaaa--gtcttcttttacaagagatgtt-tagaaaatttattttggggattttgcgtatattgttttgcgcatctttctcaccatgagagttttcccgtggttttgcag
          ||| ||||| || ||| | || || ||  | || |||  ||  || ||||||||||| ||  | |||||||||||||||||||| ||||||| |  | ||    |   | |   |||   |||  |  ||   || |    | || | |||    ||  || ||   || |||| ||  |||||                                
----------GTCTAGCATCTTTGATGCGAAGGCTGGCATTGCCTTGAACGGCAACTTTGTGAAGCTTGTGTCCTGGTACGACAACGAGTGGGGATACAGgttagtagttgcctctacagatcatctgactttgaactagggcttgtgtgcacttcaatttctaaatcctg-gt---ttattttccgtttcttttcag----------------------------

upper sequence: PP1S9_47V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA04G36870.1 (Glycine max), 5'ss of exon 11
GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtgatcactttttccactaaagtcttcttttacaagaga-tgtttagaaaatttattttggggattttgcgtatattgttttgcgcatctttctcaccatgagagttttcccgt-ggttttgcag--------------------------------
           || || ||||| ||| | || || ||| | || |||    | || ||||||||||| ||| | |||||||||||||||||||| ||||||| |  |  |   ||  |||  | ||||| ||   || | |  |  |  | | | |      | | ||   |           |  |||   |  |   |    | |||    |   ||  ||                                  
----------ATCAAGTATTTTTGATGCAAAGGCTGGAATTGCATTGAATAAGAACTTTGTGAAGCTTGTTTCTTGGTACGACAACGAGTGGGGATACAGgtaa--atgtacacctttaaccttttcttgtatgtgatagtagtgggttagtgtgtcaataagttcttaattcggccaaaaatctaatcacgcgaaatttagatgctttattattaattcagctagatctaataccttcttgtccctggttctgcag

upper sequence: PP1S9_47V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA06G18110.1 (Glycine max), 5'ss of exon 11
GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtga--tcactttttccact------------aaagtc------ttcttttacaag------agatgtttagaaaatttattttggggattttgcgtatattgtt-ttgcgcatctttctcaccatgagagttttcccgt----ggttttgcag
           || || ||||| ||| | || || ||| | || |||    | || ||||||||||| ||| | |||||||||||||||||||| ||||||| |   ||| |||  || |            | |||       | | |  | |||      |  ||   | |||  | ||     | |||||   |   || || ||    ||    ||     | | |  ||    ||    |||| |||||
----------ATCAAGTATTTTTGATGCAAAGGCTGGAATTGCATTGAATAAGAACTTTGTGAAGCTTGTTTCTTGGTACGACAACGAGTGGGGATACAGgtaaatgcacctttaacattttcttgtatgtgatagtgggttagtgcgtcaataagttgttaatttggccaaaaatctaatcacccgaattttagatgctttattattattaattcagctggttctaataccttctttgtccccggttctgcag

upper sequence: PP1S9_47V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 11
GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtga---tca-ctttttccactaa--agtcttcttttacaagagat----gtttagaaaatttat---tttggggattttgcg--tatattgttttgcgcatctttctcaccatgagagttttcccgtggttttgcag---------------------------------------------------------
           || ||||| || ||| |||| || ||| | ||  ||   |  |||||| |||| |||||  ||||||| |||||||| ||||||||||||| |   ||| |  | |  | |||  |  || | |  ||  |||||     ||    | ||| ||   |||| ||  | |||     ||  ||   | | |  |   ||||  |  |  ||  ||  |  ||   |                                                           
----------ATCAAGCATCTTTGATGCCAAGGCTGGAATTGCCCTGAATGCCAATTTTTTGAAACTCGTCTCGTGGTATGACAACGAATGGGGTTACAGgtaaatttcagccctcttgattaatcaagctacataaacccgagattatcattcgatacattgatagatttgaggcctctgcagccttagagtagagaggacatgaatcacatttggcattgccctttaattaatccctctaagctttgatgattgattgctgaaatcctttttctcgtatgttttactttgcag

upper sequence: PP1S9_47V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 10
GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtgatcactttttccactaaagtcttcttttacaagagatgtttagaaaatttattttggggattttgcgtatattgttttgcgcatctttctcaccatgagagttttcccgtggttttgcag
| || |||||||| ||||| |||||  |||  || ||| |||| |||  |||  | ||||| ||||| ||||||||||| |||||||| ||||| ||||||||      ||||     |   |||  | ||      ||| || |     ||| ||||  | |                                                            
GTGACAGCCGGTCGAGCATCTTCGACGCCAGCGCTGGAATCGCCTTGAACGACCACTTTGTAAAGCTGGTTGCGTGGTATGACAACGAATGGGGCTACAGgtgggaggattttgtcgcagtttctggtgtt------gatcttcactttttttcttttttgcag-----------------------------------------------------------

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|162182673|gb|FC360343.1|FC360343
EST:     GAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAG                         CCACCGGGTGCTGGATCTCATCATGCACATGTCATCAGTGCAACATTCTCG
genomic: GAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtgatcactt ... ggttttgcagCCACCGGGTGCTGGATCTCATCATGCACATGTCATCAGTGCAACATTCTCG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGATAGCCGGTCCAGCATTTTCGATTCCAAAGCAGGATTCGCTTTGGCCGAAAATTTTGTGAAGCTCGTTGCGTGGTACGACAACGAGTGGGGTTACAGgtgatcactttttccactaaagtcttcttttacaagagatgtttagaaaatttattttggggattttgcgtatattgttttgcgcatctttctcaccatgagagttttcccgtggttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC