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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcattttttttctctttttttttcccctccgtttttctttttccttcacccatagaagatgcttgatatgattatactgtttcttgaatgtcttttcatatcaacagagcttgatttagcctgcttcagccttcctcctcaatgggctcgtaacaaagaatgattgaaattgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTTCAGCTTCTG

Basic information

species Physcomitrella patens
transcript PP1S4_12V6.1
intron # 8
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|162178865|gb|FC354797.1|FC354797
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162159187|gb|FC334358.1|FC334358
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|100375450|gb|BY948872.1|BY948872
EST:     TTGATGTAGAGGTGTTTCGACTCA-CTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCCAGTT
genomic: TTGATGTAGAGGTGTT-CGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|67568839|gb|BJ941663.1|BJ941663
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGAT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGAT
EST: gi|162175775|gb|FC352077.1|FC352077
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162198744|gb|FC374227.1|FC374227
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|208351568|gb|DC909998.1|DC909998
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATT-GATTACCANCCC-AAGTN
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162257953|gb|FC433839.1|FC433839
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162185024|gb|FC362470.1|FC362470
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
EST: gi|162276463|gb|FC452466.1|FC452466
EST:     TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAA                         GACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT
genomic: TTTGATGTAGAGGTGTTCGACTCAACTGAGGACTATGTGAAGTTGATGAAgtgagcattt ... tgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagccttcctcctcaatgggctcgtaacaaagaatgattgaaattgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTTCAGCTTCTG
                                     attgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcattttttttctctttttttttcccctccgtttttctttttccttcacccatagaagatgcttgatatgattatactgtttcttgaatgtcttttcatatcaacagagcttgatttagcctgcttcagccttcctcctcaatgggctcgtaacaaagaatgattgaaattgatgttcagGACTATTTTCGACTTCACAGCGATCAAGGATTTGATTACCAACCCCAAGTTCAGCTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT