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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgaagcaaaatgcagtaaatgaaaacatggtggaattccctgtaatggtttatgttcttgcaaccttttaatttctatgtttaaaaatcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCCAATTGATTCTAGTGTCTAA

Basic information

species Physcomitrella patens
transcript PP1S209_135V6.1
intron # 11
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|162268242|gb|FC444531.1|FC444531
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|37824726|gb|BJ582792.1|BJ582792
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|22491904|gb|BU051827.1|BU051827
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCTATTTATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|162268243|gb|FC444532.1|FC444532
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|162242621|gb|FC414999.1|FC414999
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|67694398|gb|BJ954631.1|BJ954631
EST:     GCAGCTGCAGTNGCTTTGCGTTTGGCCAAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: GCAGCTGCAGTTGCTTTGCGTTTGGCC-AAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|37827697|gb|BJ585709.1|BJ585709
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|162244830|gb|FC420182.1|FC420182
EST:     CAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: CAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|37843464|gb|BJ601472.1|BJ601472
EST:     CAGCTGCAGTTGCTTTGCGTTTGNCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: CAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|162156562|gb|FC332170.1|FC332170
EST:     GCAGCTGCAGTTGC-TTGCGTTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: GCAGCTGCAGTTGCTTTGCG-TTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|37850470|gb|BJ608478.1|BJ608478
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|162242620|gb|FC414998.1|FC414998
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|162194101|gb|FC370276.1|FC370276
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|162185218|gb|FC361728.1|FC361728
EST:     AGCAGCTGCAGTTGCTATGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
EST: gi|162242623|gb|FC415001.1|FC415001
EST:     AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTG                         AATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC
genomic: AGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 35 (downstream exon)
Score: 17

CTGAATACATCGGTTTTATTGGAGGCTTTCGAGGCAAGGTCTGCCCGTCAAGCAGCTGCAGTTGCTTTGCGTTTGGCCAAGGGATCGGGATCAGAAGCTGgtgtgttaca ... tcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCCAATTGATTCTAGTGTCTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatggtttatgttcttgcaaccttttaatttctatgtttaaaaatcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCCAATTGATTCTAGTGTCTAA
                       ttttaat  putative branch site (score: 17)
                       ttttaatttctatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgaagcaaaatgcagtaaatgaaaacatggtggaattccctgtaatggtttatgttcttgcaaccttttaatttctatgtttaaaaatcttggacagAATTCCAAGAAAACACGCCTGAACTGGTGGAATCAGCTCGTGCTCATTGCCAATTGATTCTAGTGTCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC