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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtgtggaactcggggtgactcgattttcaaaaaccctggtggtctttgatcagacattttgttcatttccagcatagattctcccacacttcagattgtctaactcatctgtttgtggatgtatgcgtgtgtctctcccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAACATAGACGCAACGCCCTTCACACTGCAAGGGGAGCCAGCTGGGTTGGGAA

Basic information

species Physcomitrella patens
transcript PP1S4_121V6.1
intron # 1
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|208400761|gb|DC904939.1|DC904939
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100436779|gb|BY979521.1|BY979521
EST:     TCATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: TCATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100398015|gb|BY954045.1|BY954045
EST:     ATCATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATCATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100377110|gb|BY968368.1|BY968368
EST:     ATCATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATCATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100436689|gb|BY979476.1|BY979476
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100447954|gb|CJ972253.1|CJ972253
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|67718538|gb|BJ968797.1|BJ968797
EST:     GCACTTTGCAACACATCATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: GCACTTTGCAACACATCATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|67703627|gb|BJ963860.1|BJ963860
EST:     ATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|208355688|gb|DC929952.1|DC929952
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100435313|gb|BY979180.1|BY979180
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100451519|gb|CJ974807.1|CJ974807
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100426284|gb|BY958820.1|BY958820
EST:     TTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAGCAAGAAC
genomic: TTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|208385250|gb|DC915050.1|DC915050
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100394952|gb|BY990007.1|BY990007
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100372181|gb|BY985473.1|BY985473
EST:     ATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100374910|gb|BY949119.1|BY949119
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|67709350|gb|BJ965166.1|BJ965166
EST:     ATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100438655|gb|BY961735.1|BY961735
EST:     ATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100428115|gb|BY959290.1|BY959290
EST:     TTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: TTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|67716302|gb|BJ966562.1|BJ966562
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100388270|gb|BY951872.1|BY951872
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
EST: gi|100379825|gb|BY949963.1|BY949963
EST:     ATTATCATTTTTGAGTTGCGATCAATCTCTCTG                         CTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC
genomic: ATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAAC

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: 25 (upstream exon), 35 (downstream exon)
Score: 9

ATATGTTTTGCACTTTGCAACACATCATTATCATTTTTGAGTTGCGATCAATCTCTCTGgtcagtgtgt ... cccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAACATAGACGCAACGCCCTTCACACTGCAAGGGGAGCCAGCTGGGTTGGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagattgtctaactcatctgtttgtggatgtatgcgtgtgtctctcccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAACATAGACGCAACGCCCTTCACACTGCAAGGGGAGCCAGCTGGGTTGGGAA
      gtctaac  putative branch site (score: 9)
                                    tgtgtctctcccttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgtgtggaactcggggtgactcgattttcaaaaaccctggtggtctttgatcagacattttgttcatttccagcatagattctcccacacttcagattgtctaactcatctgtttgtggatgtatgcgtgtgtctctcccttcacagCTTTCTCAACTTGGGATTCGATTCTTCTGGTAAACTATGGAGAACAAGAACATAGACGCAACGCCCTTCACACTGCAAGGGGAGCCAGCTGGGTTGGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG