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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgcacttgtcaagagtagacctacttcctcggtgttcgtaagatgttgcaaatgcttgctatgtcaaggacgtagtatctttttttgaacgtgtctttttatttcagataatcatggatcagttgtctttgtattcgattgaagtgttgaatttttgtttatgttcgtggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGCTATCAGCTCGATATGCGCACATTCGATGAGCTTTCAGACGGAGAATATG

Basic information

species Physcomitrella patens
transcript PP1S90_83V6.1
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|37849529|gb|BJ607537.1|BJ607537
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|162151737|gb|FC328594.1|FC328594
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|162177195|gb|FC352624.1|FC352624
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|208355081|gb|DC922197.1|DC922197
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|37846836|gb|BJ604844.1|BJ604844
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|37842133|gb|BJ600141.1|BJ600141
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|67721373|gb|BJ971632.1|BJ971632
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|37849553|gb|BJ607561.1|BJ607561
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|37822279|gb|BJ580345.1|BJ580345
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|162186114|gb|FC361318.1|FC361318
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|37839909|gb|BJ597917.1|BJ597917
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|37834574|gb|BJ592586.1|BJ592586
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|162177196|gb|FC352625.1|FC352625
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|37840093|gb|BJ598101.1|BJ598101
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|37841281|gb|BJ599289.1|BJ599289
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
EST: gi|67724967|gb|BJ975226.1|BJ975226
EST:     AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAG                         GAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC
genomic: AGTACAAGCGGTTTGGATGTACGTTAGAATTTGTTACGAACAAGTCACAGgtgcgtgcac ... tggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctttgtattcgattgaagtgttgaatttttgtttatgttcgtggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGCTATCAGCTCGATATGCGCACATTCGATGAGCTTTCAGACGGAGAATATG
                                                ttttc  CT-rich tract
                        ttgaatttttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgcacttgtcaagagtagacctacttcctcggtgttcgtaagatgttgcaaatgcttgctatgtcaaggacgtagtatctttttttgaacgtgtctttttatttcagataatcatggatcagttgtctttgtattcgattgaagtgttgaatttttgtttatgttcgtggttttcagGAAGGATCACAGTTTTGTCGTGGTTTTGGTGGAATTGGAGGAATCTTGCGCTATCAGCTCGATATGCGCACATTCGATGAGCTTTCAGACGGAGAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA