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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcatttttcaggggctgtgggacttgctttgattttcattccggtggtcgatctagtggttctggtattgtcatgtggttttgcgattgaacgatgtgagtaacggggaactttttactcgcagagaagcaattcatctgatgtttgtgaggtgctaatgtgtgtggttcagTGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGCAATGGCGGAATTCCGACCCGCACAAGAGCAGTCGCAGCACCCTGGAGAG

Basic information

species Physcomitrella patens
transcript PP1S6_369V6.1
intron # 1
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|100427649|gb|BY977603.1|BY977603
EST:     GTGAATTCCATTCTCGTATTGCACCGAACAAGAACTTTTCTGTTGACCAG                         TGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGC
genomic: GTGAATTCCATTCTCGTATTGCACCGAACAAGAACTTTTCTGTTGACCAGgtaggcattt ... tgtggttcagTGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGC
EST: gi|100442466|gb|BY963160.1|BY963160
EST:     GTGAATTCCATTCTCGTATTGCACCGAACAAGAACTTTTCTGTTGACCAG                         TGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGC
genomic: GTGAATTCCATTCTCGTATTGCACCGAACAAGAACTTTTCTGTTGACCAGgtaggcattt ... tgtggttcagTGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGC
EST: gi|100416309|gb|BY975327.1|BY975327
EST:     GTGAATTCCATTCTCGTATTGCACCGAACAAGAACTTTTCTGTTGACCAG                         TGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGC
genomic: GTGAATTCCATTCTCGTATTGCACCGAACAAGAACTTTTCTGTTGACCAGgtaggcattt ... tgtggttcagTGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgcagagaagcaattcatctgatgtttgtgaggtgctaatgtgtgtggttcagTGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGCAATGGCGGAATTCCGACCCGCACAAGAGCAGTCGCAGCACCCTGGAGAG
                                   tgctaat  putative branch site (score: 2)
             aattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcatttttcaggggctgtgggacttgctttgattttcattccggtggtcgatctagtggttctggtattgtcatgtggttttgcgattgaacgatgtgagtaacggggaactttttactcgcagagaagcaattcatctgatgtttgtgaggtgctaatgtgtgtggttcagTGATCTTGAATCTTTCGTAAATTTTAGCTGTAGTCGGATTTACGTTTTCGCAATGGCGGAATTCCGACCCGCACAAGAGCAGTCGCAGCACCCTGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA