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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttttgaaccgattcctctgaatttgaagctggaatggtaacagatgtgagccgtattaggatggcttttattgatgaaagtgtattgaataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT

Basic information

species Physcomitrella patens
transcript PP1S90_139V6.2
intron # 4
splice site 3'
intron type U2

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|162163706|gb|FC339785.1|FC339785
EST:     CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAG                         GACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
genomic: CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
EST: gi|162209803|gb|FC385737.1|FC385737
EST:     CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAG                         GACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
genomic: CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
EST: gi|162279385|gb|FC455932.1|FC455932
EST:     CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAG                         GACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
genomic: CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
EST: gi|67698886|gb|BJ959119.1|BJ959119
EST:     CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAG                         GACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
genomic: CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
EST: gi|100378011|gb|BY949635.1|BY949635
EST:     CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAG                         GACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
genomic: CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
EST: gi|100361031|gb|BY946879.1|BY946879
EST:     CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAG                         GACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
genomic: CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
EST: gi|100378215|gb|BY949738.1|BY949738
EST:     TGTNAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTTGAG                         -ACGGAGATATTATTTATATTGACGTCACAGTCTGGGTAAAT
genomic: TGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTT-GAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
EST: gi|37828378|gb|BJ586390.1|BJ586390
EST:     CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAG                         GACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
genomic: CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
EST: gi|37848383|gb|BJ606391.1|BJ606391
EST:     CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAG                         GACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
genomic: CTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttgg ... aataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgagccgtattaggatggcttttattgatgaaagtgtattgaataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT
                          tattgat  putative branch site (score: 3)
                       ttttattgatgaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttttgaaccgattcctctgaatttgaagctggaatggtaacagatgtgagccgtattaggatggcttttattgatgaaagtgtattgaataatgcagGACGGAGATATTATTAATATTGACGTCACAGTCTGGTTAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT