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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtacgattaagtctgaattttattgtacactcaaatactatattttgaattctgttatgaattttggaacagagtccgataatttctactgatttacttggtttttgttttttgcacgtttatctcaaagTGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCAGAGACTCACCGTGGG

Basic information

species Physcomitrella patens
transcript PP1S9_317V6.2
intron # 3
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|100406113|gb|BY991546.1|BY991546
EST:     GCCAGCAATTAGCTTATTTGGGTCCCTCGCCTGATCATGTTCTGAATGTG                         TGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA
genomic: GCCAGCAATTAGCTTATTTGGGTCCCTCGCCTGATCATGTTCTGAATGTGgtgagtgtac ... tatctcaaagTGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA
EST: gi|208396371|gb|DC911946.1|DC911946
EST:     GCCAGCAATTAGCTTATTTGGGTCCCTCGCCTGATCATGTTCTGAATGTG                         TGGGTACGCCCGCTTCATGGCACAGACGANGAGGCCAAGATGATAACTGCA
genomic: GCCAGCAATTAGCTTATTTGGGTCCCTCGCCTGATCATGTTCTGAATGTGgtgagtgtac ... tatctcaaagTGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA
EST: gi|100356505|gb|BY946399.1|BY946399
EST:     GCCAGCAATTAGCTTATTTGGGTCCCTCGCCTGATCATGTTCTGAATGTG                         TGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA
genomic: GCCAGCAATTAGCTTATTTGGGTCCCTCGCCTGATCATGTTCTGAATGTGgtgagtgtac ... tatctcaaagTGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA
EST: gi|162252662|gb|FC428699.1|FC428699
EST:     CGCCTGATCATGTTCTGAATGTG                         TGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA
genomic: CGCCTGATCATGTTCTGAATGTGgtgagtgtac ... tatctcaaagTGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA
EST: gi|100418237|gb|BY993400.1|BY993400
EST:     GCCAGCAATTAGCTTATTTGGGTCCCTCGCCTGATCATGTTCTGAATGTG                         TGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA
genomic: GCCAGCAATTAGCTTATTTGGGTCCCTCGCCTGATCATGTTCTGAATGTGgtgagtgtac ... tatctcaaagTGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgataatttctactgatttacttggtttttgttttttgcacgtttatctcaaagTGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCAGAGACTCACCGTGGG
           tactgat  putative branch site (score: 2)
                                           tttatctc  putative PPT
                          tttttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtacgattaagtctgaattttattgtacactcaaatactatattttgaattctgttatgaattttggaacagagtccgataatttctactgatttacttggtttttgttttttgcacgtttatctcaaagTGGGTACGCCCGCTTCATGGCACAGACGAGGAGGCCAAGATGATAACTGCAGAGACTCACCGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG