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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacactggaagtattaaatactggaagattccagcccttctgcaatttcttgatgttgcgtctgggagaagttacaagttgtgagtagtcctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACATCCAGATGTGTATGAGCCCTGTGATGACTCCTTCGCTCTGGTTGATGCGT

Basic information

species Physcomitrella patens
transcript PP1S78_28V6.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S78_28V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G121840_T01 (Zea mays), 3'ss of exon 1
--------------aacactg-gaagtattaaatactggaagattccagcccttctgcaatttcttgatgttgcgtctgggagaagttacaagttgtgagtagtcctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACATCCAGATGTGTATGAGCCCTGTGATGACTCCTTCGCTCTGGTTGATGCGT
              ||||  | | |  | || |||   | |   |  |    ||     | |   | ||| |   | |  || ||      | || ||     | ||  ||| |||       |   | |||   ||        || | ||| || |   | |||||||||||||||||||| |||||||| ||||| || || |||||||   
atgtgtttgctttaaacagagaggaaaaatagatatgtgtaagctatatttatttaaggaatctct-atgctatttttatgacaaaagcttatttttgcagGCTTCTTCTGGGAGGACAT---TAAACACCGCACAA--------ATTCCGCTTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG---

upper sequence: PP1S78_28V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G463983_T01 (Zea mays), 3'ss of exon 2
--------------aacactg-gaagtattaaatactggaagattccagcccttctgcaatttcttgatgttgcgtctgggagaagttacaagttgtgagtagtcctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACATCCAGATGTGTATGAGCCCTGTGATGACTCCTTCGCTCTGGTTGATGCGT
              ||||  | | |  | || |||   | |   |  |    ||     | |   | ||| |   | |  || ||      | || ||     | ||  ||| |||       |   | ||    || | | ||        | || |   | |||||||||||||||||||| |||||||| ||||| || || |||||||   
atgtgcttgctttaaacagagaggaaaaatagatatgtgtaagctatatttatttaaggaatctct-atgctatttttatgacaaaagcttatttttgcagGCTTCTTCTGGGAGGACAT---TAAACACCACACAAATTCCTC--------TTGTTGCGAGCCATCCAGATGTGTATGAGCCATGTGATGATTCCTTTGCCCTTGTTGATG---
















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|67572748|gb|BJ945572.1|BJ945572
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|100372882|gb|BY948747.1|BY948747
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|18368836|gb|BJ200921.1|BJ200921
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|100410263|gb|BY974490.1|BY974490
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|100359380|gb|BY965718.1|BY965718
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|22492275|gb|BU052198.1|BU052198
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCTTCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|18351757|gb|BJ183809.1|BJ183809
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|162156875|gb|FC333029.1|FC333029
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|100363006|gb|BY984310.1|BY984310
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         T
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcag-
EST: gi|100363006|gb|BY984310.1|BY984310
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         T
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcag-
EST: gi|100363006|gb|BY984310.1|BY984310
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         T
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcag-
EST: gi|100363006|gb|BY984310.1|BY984310
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         T
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcag-
EST: gi|100363006|gb|BY984310.1|BY984310
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         T
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcag-
EST: gi|100363006|gb|BY984310.1|BY984310
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         T
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcag-
EST: gi|100363006|gb|BY984310.1|BY984310
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         T
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcag-
EST: gi|100363006|gb|BY984310.1|BY984310
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         T
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcag-
EST: gi|22133203|gb|BQ827604.1|BQ827604
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|100447930|gb|CJ972229.1|CJ972229
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|100380393|gb|BY986677.1|BY986677
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|18345516|gb|BJ177559.1|BJ177559
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|18348820|gb|BJ180869.1|BJ180869
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|18366225|gb|BJ198303.1|BJ198303
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
EST: gi|67573276|gb|BJ946100.1|BJ946100
EST:     CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTC                         GGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT
genomic: CGCCTTCAAGCCTGCGTATCAGCCGGGTTAGAGAGCAGCGGAAGTCTTTCgtaagttttc ... ctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttgatgttgcgtctgggagaagttacaagttgtgagtagtcctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACATCCAGATGTGTATGAGCCCTGTGATGACTCCTTCGCTCTGGTTGATGCGT
  tcttgat  putative branch site (score: 4)
                                           tcctcat  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacactggaagtattaaatactggaagattccagcccttctgcaatttcttgatgttgcgtctgggagaagttacaagttgtgagtagtcctcatggcagGGTGCATCTCCGCGCCGGCGAAGTGCGTCCATCCGGCTGGTAGGTCGACATCCAGATGTGTATGAGCCCTGTGATGACTCCTTCGCTCTGGTTGATGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG