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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaatctcatcttaagagcatagttcgaatgttggtttctatgtacatacagtcagaagttcacaaatgtaatgacgctgtactgcaacgtgtctggcttgatgctgtcacagcctgtaaaattgctggaaacggataatcccactaatatatgtttcaactggcgatctgcag

Basic information

species Physcomitrella patens
transcript PP1S272_13V6.5
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S272_13V6.5 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os10g33270.1 (Oryza sativa), 5'ss of exon 2
GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaatctcatcttaagagcatagttcgaatgttggtttctatgtacatacagtcagaagttcacaaatgtaatgacgctgt--actgcaacgtgtctggcttgatgctgtcacagcctgtaaaattgctggaaacggataatcccactaatatatgtttcaactggcgatctgcag
  || | |||||   | | ||||  || || ||||||||||| || |||||||| ||||||||||| || |||||||   || ||  | || |  | |  ||| | |  || |||  || |||       ||| | |||   | | |  ||   |||   ||||||    | |    || | | |                                                                    
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAATgtaag---atatctgcctatg--cttcattctatt--tgattttcatttaccc-----cagtatttcttgact-tcctgttcctggtaactgcacatggacgaagttaaggat--------------------------------------------------------------------

upper sequence: PP1S272_13V6.5 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 2
GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaatctcatcttaagagcatagttcgaatgttggtttctatgtacatacagtcagaagttcacaaatgtaatgacgctgtactgcaacgtgtctggcttgatgctgtcacagcctgtaaaattgctggaaacggataatcccactaatatatgtttcaactggcgatctgcag
  || | |||||   | | ||||  || || ||||||||||| ||||||||||| ||||||||||| || ||||||| | ||  ||      | || |  ||      |   || || | | |    | || |   |  || | | |  |||    ||     ||    |  |   ||||                                                                       
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaag-agatacca------gtgcttcatttatgcataaattcctgt-tcctggtaatctggcatgaactattatg-tgatatagttagtaaatccattagttatgatt----------------------------------------------------------------------

upper sequence: PP1S272_13V6.5 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv05s0049g01520.t01 (Vitis vinifera), 5'ss of exon 2
GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaatctcatcttaagagcatagttcgaatgttggtttctatgtacatacagtcagaagttcacaaatgtaatgacgctgtactgcaacgtgtctggcttgatgctgtcacagcctgtaaaattgctggaaacggataatcccactaatatatgtttcaactggcgatctgcag
  || | |||||     | ||||  || || ||||||||||| || |||||||| |||||||| || |||||||||||   | |  |||      |  | ||    |||| | ||      ||||  | |    ||        | | |  ||| | |     |||  || |  |   ||                                                                       
ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCATgtaagtctttttggtct------cccaatttctctgtttgcttgc-cacacatgtacttttgagcctg----tttgacaacggtttctgaaaacaggtttc-ccaaatttca-------------------------------------------------------------------

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|162205230|gb|FC380912.1|FC380912
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162239982|gb|FC418785.1|FC418785
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67697134|gb|BJ957367.1|BJ957367
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67701145|gb|BJ961378.1|BJ961378
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67573748|gb|BJ946572.1|BJ946572
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67693986|gb|BJ954219.1|BJ954219
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67700516|gb|BJ960749.1|BJ960749
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67692354|gb|BJ952587.1|BJ952587
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|18361453|gb|BJ193519.1|BJ193519
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162239983|gb|FC418786.1|FC418786
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67701515|gb|BJ961748.1|BJ961748
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|37842305|gb|BJ600313.1|BJ600313
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162219374|gb|FC396904.1|FC396904
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67508506|gb|BJ941371.1|BJ941371
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|208395581|gb|DC928996.1|DC928996
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67693480|gb|BJ953713.1|BJ953713
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162222811|gb|FC399065.1|FC399065
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67569108|gb|BJ941932.1|BJ941932
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162162852|gb|FC338101.1|FC338101
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67700294|gb|BJ960527.1|BJ960527
EST:     ACNGCGAAANGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: ACGGCGAAA-GCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|37850310|gb|BJ608318.1|BJ608318
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162246985|gb|FC424785.1|FC424785
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|18366564|gb|BJ198643.1|BJ198643
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGA
EST: gi|37849018|gb|BJ607026.1|BJ607026
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|208367515|gb|DC955695.1|DC955695
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162205229|gb|FC380911.1|FC380911
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|37846944|gb|BJ604952.1|BJ604952
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162161409|gb|FC337615.1|FC337615
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|67692348|gb|BJ952581.1|BJ952581
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
EST: gi|162247194|gb|FC420236.1|FC420236
EST:     TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCAT                         TATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA
genomic: TACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaat ... cgatctgcagTATGTCTGCCATTGGTTACTACTGCTCTGTAGAGAAGGTGAAAGGCAAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCACGAAGCGACTGTACATTACGGCGAAAGCATCAAGGATATCATCAATGAAGAGTTTGGTGACGGCATgtaagtaaatctcatcttaagagcatagttcgaatgttggtttctatgtacatacagtcagaagttcacaaatgtaatgacgctgtactgcaacgtgtctggcttgatgctgtcacagcctgtaaaattgctggaaacggataatcccactaatatatgtttcaactggcgatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA