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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagatccacattcactcgaacattggctttcattagcttctgcataacatttgagaacggtatgttggacatttggcattgacagcgtgatgcatgacctttttgtgggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAGAAAAGGAACGAGAGCCACATGAACACGGGATTCTCTTTCGTGGATGCAT

Basic information

species Physcomitrella patens
transcript PP1S55_167V6.3
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|208380736|gb|DC919438.1|DC919438
EST:     GGCAATGGCCGAAGTTTGTACAAG                         AATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
genomic: GGCAATGGCCGAAGTTTGTACAAGgtgaagatcc ... ggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
EST: gi|208392948|gb|DC928634.1|DC928634
EST:     TCCAAGGCTCCATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAG                         AATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
genomic: TCCAAGGCTCCATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAGgtgaagatcc ... ggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
EST: gi|100428241|gb|BY977704.1|BY977704
EST:     TCCAAGGCTCCATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAG                         AATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
genomic: TCCAAGGCTCCATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAGgtgaagatcc ... ggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
EST: gi|100445957|gb|CJ970256.1|CJ970256
EST:     TCCAAGGCTCCATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAG                         AATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAN
genomic: TCCAAGGCTCCATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAGgtgaagatcc ... ggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
EST: gi|208381164|gb|DC923729.1|DC923729
EST:     AATGGCCGAAGTTTGTACAAG                         AATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
genomic: AATGGCCGAAGTTTGTACAAGgtgaagatcc ... ggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
EST: gi|208380688|gb|DC919418.1|DC919418
EST:     ATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAG                         AATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
genomic: ATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAGgtgaagatcc ... ggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
EST: gi|208381526|gb|DC923112.1|DC923112
EST:     CGAAGTTTGTACAAG                         AATTGCCATNTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
genomic: CGAAGTTTGTACAAGgtgaagatcc ... ggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
EST: gi|208356793|gb|DC926804.1|DC926804
EST:     TCCAAGGCTCCATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAG                         AATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG
genomic: TCCAAGGCTCCATCGACTTTGTTTTCGGCAATGGCCGAAGTTTGTACAAGgtgaagatcc ... ggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggacatttggcattgacagcgtgatgcatgacctttttgtgggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAGAAAAGGAACGAGAGCCACATGAACACGGGATTCTCTTTCGTGGATGCAT
              cattgac  putative branch site (score: 3)
                                     tttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagatccacattcactcgaacattggctttcattagcttctgcataacatttgagaacggtatgttggacatttggcattgacagcgtgatgcatgacctttttgtgggttacgcagAATTGCCATCTGCACTCGGAGGCGAAGGTCTTCGGTTCCGTGACGGCTCAGAAAAGGAACGAGAGCCACATGAACACGGGATTCTCTTTCGTGGATGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA