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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgccaccgagcccctcatcttccaagttacgctagctctatgtgctgttcattatctcctctccttgttcgatgatcacatgtactttgggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCCTGACGATGAAACAGGCCGTTCTG

Basic information

species Physcomitrella patens
transcript PP1S100_198V6.2
intron # 2
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|18326001|gb|BJ158000.1|BJ158000
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18361423|gb|BJ193489.1|BJ193489
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18325506|gb|BJ157503.1|BJ157503
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18330350|gb|BJ162356.1|BJ162356
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCCACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18325613|gb|BJ157610.1|BJ157610
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18332063|gb|BJ164075.1|BJ164075
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18329694|gb|BJ161700.1|BJ161700
EST:     GTTCGTGGTCATTGGTGCCTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18330259|gb|BJ162265.1|BJ162265
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18328969|gb|BJ160975.1|BJ160975
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18374420|gb|BJ205998.1|BJ205998
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18329368|gb|BJ161374.1|BJ161374
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18347749|gb|BJ179796.1|BJ179796
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18351974|gb|BJ184026.1|BJ184026
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18344180|gb|BJ176219.1|BJ176219
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18332289|gb|BJ164302.1|BJ164302
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18359780|gb|BJ191841.1|BJ191841
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18355771|gb|BJ187830.1|BJ187830
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18325798|gb|BJ157795.1|BJ157795
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18328115|gb|BJ160119.1|BJ160119
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18369497|gb|BJ201584.1|BJ201584
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18367200|gb|BJ199281.1|BJ199281
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18358412|gb|BJ190471.1|BJ190471
EST:     GTTCGTGGTCATTGGTGCTTTTGCGGCCTTTGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18351328|gb|BJ183380.1|BJ183380
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18326157|gb|BJ158156.1|BJ158156
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18367452|gb|BJ199535.1|BJ199535
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18349364|gb|BJ181413.1|BJ181413
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18353077|gb|BJ185132.1|BJ185132
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18330492|gb|BJ162498.1|BJ162498
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
EST: gi|18328497|gb|BJ160502.1|BJ160502
EST:     GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATG                         GAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC
genomic: GTTCGTGGTCATTGGTGCGTTTGCGGCCTTCGGGTTCGGCTGGGGAAATGgtaagttcac ... gggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgttcattatctcctctccttgttcgatgatcacatgtactttgggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCCTGACGATGAAACAGGCCGTTCTG
     tcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgccaccgagcccctcatcttccaagttacgctagctctatgtgctgttcattatctcctctccttgttcgatgatcacatgtactttgggtgtgcagGAGCGAATGACTTGGCAAATGGGTTCGCTACCTCGGTGGGAAGCAAGACCCTGACGATGAAACAGGCCGTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA