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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgttgaagggggtaatacatacgccgattatcttatacagtttgacagtttggctctggtctgtgctttatgtgggtgacaattgcatacttattacttctgtaatgtgaggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGTGGTCCCGACGAG

Basic information

species Physcomitrella patens
transcript PP1S168_70V6.1
intron # 5
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|208391163|gb|DC942075.1|DC942075
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|18360636|gb|BJ192699.1|BJ192699
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|100386703|gb|BY970244.1|BY970244
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|162194861|gb|FC370525.1|FC370525
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGGAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|162223684|gb|FC399457.1|FC399457
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|18345963|gb|BJ178006.1|BJ178006
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCA
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCA
EST: gi|100405914|gb|BY991447.1|BY991447
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|162162825|gb|FC338087.1|FC338087
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|18365419|gb|BJ197494.1|BJ197494
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|162181557|gb|FC358171.1|FC358171
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|18346813|gb|BJ178858.1|BJ178858
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|18369304|gb|BJ201390.1|BJ201390
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|18366141|gb|BJ198219.1|BJ198219
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|18371368|gb|BJ202970.1|BJ202970
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|100368990|gb|BY984972.1|BY984972
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|162193559|gb|FC370462.1|FC370462
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|208384123|gb|DC911259.1|DC911259
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|162164264|gb|FC342079.1|FC342079
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGT
EST: gi|18360603|gb|BJ192666.1|BJ192666
EST:     TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAG                         GGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTTGG
genomic: TATCCACCCCCGCTGTGTCTTCAATCATCCGAAACCGAGTTAACAGTCAGgtaggtgttg ... ggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCT-GG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatgtgggtgacaattgcatacttattacttctgtaatgtgaggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGTGGTCCCGACGAG
                     atacttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtgttgaagggggtaatacatacgccgattatcttatacagtttgacagtttggctctggtctgtgctttatgtgggtgacaattgcatacttattacttctgtaatgtgaggggtttcagGGTGAAAAGGCTTACGGGGCCTTCATTCTGACTGCCAGCCACAACCCTGGTGGTCCCGACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG